Uses of diazepane derivatives

ABSTRACT

The present invention provides compounds of Formula (II) (e.g., compounds of Formula (I)), and pharmaceutically compositions thereof. Compounds of Formula (II) are believed to be binders of bromodomains and/or bromodomain-containing proteins (e.g., bromo and extra terminal (BET) proteins). Also provided are methods, uses, and kits using the compounds and pharmaceutical compositions for inhibiting the activity (e.g., increased activity) of bromodomains and/or bromodomain-containing proteins and for treating and/or preventing in a subject diseases associated with bromodomains or bromodomain-containing proteins (e.g., proliferative diseases, cardiovascular diseases, viral infections, fibrotic diseases, metabolic diseases, endocrine diseases, and radiation poisoning). The compounds, pharmaceutical compositions, and kits are also useful for male contraception.

RELATED APPLICATION

The present application claims priority under 35 U.S.C. §119(e) to U.S.provisional patent application, U.S. Ser. No. 61/934,672, filed Jan. 31,2014, which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

Bromodomain-containing proteins are of substantial biological interest,as components of transcription factor complexes and determinants ofepigenetic memory. For example, the bromo and extra terminal (BET)protein family (e.g., bromodomain-containing protein 2 (BRD2),bromodomain-containing protein 3 (BRD3), bromodomain-containing protein4 (BRD4), and bromodomain testis-specific protein (BRDT)) shares acommon domain architecture featuring two amino-terminal bromodomainsthat exhibit high levels of sequence conservation, and a more divergentcarboxy-terminal recruitment domain (Filippakopoulos et al., Nature2010, 468, 1067-1073). BRD2 and BRD3 are reported to associate withhistones along actively transcribed genes and may be involved infacilitating transcriptional elongation (Leroy et al., Mol. Cell. 2008,30, 51-60). It has also been reported that BRD4 or BRD3 may fuse withnuclear protein in testis (NUT), forming novel fusion oncogenes BRD4-NUTor BRD3-NUT, in a highly malignant form of epithelial neoplasia (Frenchet al., Cancer Res., 2003, 63, 304-307; French et al., J. Clin. Oncol.2004, 22, 4135-4139). Data suggests that BRD-NUT fusion proteinscontribute to carcinogenesis (French et al., Oncogene 2008, 27,2237-2242). BRDT is uniquely expressed in the testes and ovary. Allfamily members of BET have been reported to have some function incontrolling or executing aspects of the cell cycle and have been shownto remain in complex with chromosomes during cell division, suggesting arole in the maintenance of epigenetic memory. In addition, some virusesmake use of BET proteins to tether their genomes to the host cellchromatin, as part of the process of viral replication (You et al., Cell2004, 117, 349-360). BRD4 appears to be involved in the recruitment ofthe pTEF-b complex to inducible genes, resulting in phosphorylation ofRNA polymerase and increased transcriptional output (Hargreaves et al.,Cell 2009, 138, 129-145). In humans, BRD2, BRD3, BRD4, and BRDT exhibitsimilar gene arrangements, domain organizations, and some functionalproperties (Wu et al., J. Biol. Chem. 2007, 282, 13141-13145).

SUMMARY OF THE INVENTION

The present invention provides compounds of Formula (II) (e.g.,compounds of Formula (I)). The compounds described herein are thought tobe binders of transcription factors, such as bromodomain-containingproteins (e.g., BET proteins) and may be useful in male contraceptionand in treating and/or preventing a wide range of diseases (e.g.,diseases associated with bromodomains, diseases associated with theactivity (e.g., aberrant activity) of bromodomains, diseases associatedwith bromodomain-containing proteins, and disease associated with theactivity (e.g., aberrant activity) of bromodomain-containing proteins).Diseases that may be treated and/or prevented by the methods of theinvention include, but are not limited to, proliferative diseases (e.g.,cancers, benign neoplasms, angiogenesis, inflammatory diseases, andautoimmune diseases), cardiovascular diseases, viral infections,fibrotic diseases, metabolic diseases, endocrine diseases, and radiationpoisoning. Also provided in the present invention are pharmaceuticalcompositions, kits, methods, and uses including or using a compounddescribed herein.

In one aspect, the present invention provides compounds of Formula (II):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein

, W, R^(B), R^(C), R^(D), R^(E), R^(F), R^(G), R^(H), and m are asdescribed herein.

In certain embodiments, a compound of Formula (II) is of Formula (I):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein

, X, Z, R^(A), and n are as described herein.

Exemplary compounds of Formula (II) include, but are not limited to:

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof.

The compounds described herein are thought to be able to bindbromodomain-containing proteins. In certain embodiments, the compoundsdescribed herein bind to a bromodomain (e.g., a bromodomain of abromodomain-containing protein). The compounds described herein mayinhibit the activity of the bromodomain-containing proteins. Thecompounds described herein may also inhibit the function of abromodomain.

In still another aspect, the present invention provides pharmaceuticalcompositions including a compound described herein, and optionally apharmaceutically acceptable excipient. In certain embodiments, thepharmaceutical compositions described herein include a therapeuticallyor prophylactically effective amount of a compound described herein. Thepharmaceutical composition may be useful for treating and/or preventinga disease in a subject in need thereof. The pharmaceutical compositionmay also be useful in inhibiting the replication of a virus, in killinga virus, in inhibiting the activity of a bromodomain-containing protein,in inhibiting the activity of a bromodomain, in inhibiting the bindingof a bromodomain of a bromodomain-containing protein to an acetylatedlysine residue of a histone or other protein, in modulating (e.g.,inhibiting) transcriptional elongation, in modulating (e.g., reducing)the level of a bromodomain-containing protein, and/or in modulating(e.g., down-regulating or inhibiting) the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein in a subject or cell.

In certain embodiments, the disease described herein is a diseaseassociated with the activity (e.g., aberrant activity (e.g., increasedactivity)) of a bromodomain-containing protein. In certain embodiments,the disease is a disease associated with the function of abromodomain-containing protein. In certain embodiments, the disease is adisease associated with the activity (e.g., aberrant activity (e.g.,increased activity)) of a bromodomain. In certain embodiments, thedisease is a disease associated with the function of a bromodomain.

In certain embodiments, the disease is a proliferative disease (e.g.,cancer, benign neoplasm, angiogenesis, an inflammatory disease, or anautoimmune disease), cardiovascular disease, viral infection, fibroticdisease, metabolic disease, endocrine disease, or radiation poisoning.

In certain embodiments, the subject is a human. In certain embodiments,the subject is a non-human animal. In certain embodiments, the cell ispresent in vitro. In certain embodiments, the cell is present in vivo.

Another aspect of the present invention relates to methods of treating adisease in a subject in need thereof.

In another aspect, the present invention provides methods of preventinga disease in a subject in need thereof.

Another aspect of the present invention relates to methods of reducingthe risk of developing a disease in a subject in need thereof.

Another aspect of the present invention relates to methods of inhibitingthe replication of a virus (e.g., human immunodeficiency virus (HIV),human papillomavirus (HPV), hepatitis C virus (HCV), herpes simplexvirus (HSV), Ebola virus, and influenza virus).

Another aspect of the present invention relates to methods of killing avirus (e.g., human immunodeficiency virus (HIV), human papillomavirus(HPV), hepatitis C virus (HCV), herpes simplex virus (HSV), Ebola virus,and influenza virus).

In another aspect, the present invention provides methods of inhibitingthe activity of a bromodomain-containing protein in a subject or cell.In certain embodiments, the activity of a bromodomain-containing proteinis aberrant or unwanted activity (e.g., an increased activity) of thebromodomain-containing protein. In certain embodiments, the activity ofthe bromodomain-containing protein is selectively inhibited (e.g., whencompared to the activity of a kinase that is different from thebromodomain-containing protein) by the methods.

In yet another aspect, the present invention provides methods ofinhibiting the activity of a bromodomain in a subject or cell. Incertain embodiments, the activity of a bromodomain being inhibited isaberrant or unwanted activity (e.g., an increased activity) of thebromodomain.

In yet another aspect, the present invention provides methods ofinhibiting the binding of a bromodomain to an acetylated lysine residueof a second protein (e.g., histone (e.g., a histone described herein))in a subject or cell. In certain embodiments, the second protein is aprotein that includes at least one acetylated lysine residue.

In still another aspect, the present invention provides methods ofmodulating the expression (e.g., transcription) of a gene that isregulated by a bromodomain-containing protein in a subject or cell. Incertain embodiments, the methods of modulating the expression (e.g.,transcription) of a gene are methods of down-regulating or inhibitingthe expression (e.g., transcription) of the gene. The method may resultin decreased levels of a gene product (e.g., RNA, protein) in a cell.

In still another aspect, the present invention provides methods ofmodulating (e.g., inhibiting) transcriptional elongation in a subject orcell.

In still another aspect, the present invention provides methods ofmodulating (e.g., reducing) the level of a bromodomain-containingprotein in a subject or cell.

The methods of the present invention include administering to thesubject, contacting a cell with, or contacting a virus with an effectiveamount of a compound or pharmaceutical composition described herein. Incertain embodiments, the effective amount is a therapeutically effectiveamount. In certain embodiments, the effective amount is aprophylactically effective amount. In certain embodiments, the methodsof the present invention further include administering to the subject,contacting a cell with, or contacting a virus with an additionalpharmaceutical agent in combination with a compound or pharmaceuticalcomposition described herein. In certain embodiments, the combination ofthe pharmaceutical agent and the compound or pharmaceutical compositiondescribed herein is synergistic.

Another aspect of the invention relates to methods of screening alibrary of compounds to identify a compound that is useful in a methodof the invention.

Another aspect of the present invention relates to kits comprising acontainer with a compound or pharmaceutical composition describedherein. The kits described herein may include a single dose or multipledoses of the compound or pharmaceutical composition described herein.The provided kits may be useful in a method of the invention. In certainembodiments, the kit further includes instructions for using the kit.

In yet another aspect, the present invention provides compounds andpharmaceutical compositions described herein for use in a method of theinvention.

In yet another aspect, the present invention provides uses of thecompounds and pharmaceutical compositions described herein in a methodof the invention.

The present application refers to various issued patent, publishedpatent applications, journal articles, and other publications, all ofwhich are incorporated herein by reference. The details of one or moreembodiments of the invention are set forth herein. Other features,objects, and advantages of the invention will be apparent from theDetailed Description, the Figures, the Examples, and the Claims.

DEFINITIONS

Definitions of specific functional groups and chemical terms aredescribed in more detail below. The chemical elements are identified inaccordance with the Periodic Table of the Elements, CAS version,Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, andspecific functional groups are generally defined as described therein.Additionally, general principles of organic chemistry, as well asspecific functional moieties and reactivity, are described in ThomasSorrell, Organic Chemistry, University Science Books, Sausalito, 1999;Smith and March, March's Advanced Organic Chemistry, 5^(th) Edition,John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive OrganicTransformations, VCH Publishers, Inc., New York, 1989; and Carruthers,Some Modern Methods of Organic Synthesis, 3^(rd) Edition, CambridgeUniversity Press, Cambridge, 1987.

Compounds described herein can comprise one or more asymmetric centers,and thus can exist in various isomeric forms, e.g., enantiomers and/ordiastereomers. For example, the compounds described herein can be in theform of an individual enantiomer, diastereomer or geometric isomer, orcan be in the form of a mixture of stereoisomers, including racemicmixtures and mixtures enriched in one or more stereoisomer. Isomers canbe isolated from mixtures by methods known to those skilled in the art,including chiral high pressure liquid chromatography (HPLC) and theformation and crystallization of chiral salts; or preferred isomers canbe prepared by asymmetric syntheses. See, for example, Jacques et al.,Enantiomers, Racemates and Resolutions (Wiley Interscience, New York,1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, Stereochemistryof Carbon Compounds (McGraw Hill, N Y, 1962); and Wilen, Tables ofResolving Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ.of Notre Dame Press, Notre Dame, Ind. 1972). The invention additionallyencompasses compounds described herein as individual isomerssubstantially free of other isomers, and alternatively, as mixtures ofvarious isomers.

When a range of values is listed, it is intended to encompass each valueand sub range within the range. For example “C₁₋₆” is intended toencompass, C₁, C₂, C₃, C₄, C₅, C₆, C₁₋₆, C₁₋₅, C₁₋₄, C₁₋₃, C₁₋₂, C₂₋₆,C₂₋₅, C₂₋₄, C₂₋₃, C₃₋₆, C₃₋₅, C₃₋₄, C₄₋₆, C₄₋₅, and C₅₋₆.

The term “aliphatic” includes both saturated and unsaturated, straightchain (i.e., unbranched), branched, acyclic, cyclic, or polycyclicaliphatic hydrocarbons, which are optionally substituted with one ormore functional groups. As will be appreciated by one of ordinary skillin the art, “aliphatic” is intended herein to include, but is notlimited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, andcycloalkynyl moieties. Thus, the term “alkyl” includes straight,branched and cyclic alkyl groups. An analogous convention applies toother generic terms such as “alkenyl”, “alkynyl”, and the like.Furthermore, the terms “alkyl”, “alkenyl”, “alkynyl”, and the likeencompass both substituted and unsubstituted groups. In certainembodiments, “lower alkyl” is used to indicate those alkyl groups(cyclic, acyclic, substituted, unsubstituted, branched or unbranched)having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employedin the invention contain 1-20 aliphatic carbon atoms. In certain otherembodiments, the alkyl, alkenyl, and alkynyl groups employed in theinvention contain 1-10 aliphatic carbon atoms. In yet other embodiments,the alkyl, alkenyl, and alkynyl groups employed in the invention contain1-8 aliphatic carbon atoms. In still other embodiments, the alkyl,alkenyl, and alkynyl groups employed in the invention contain 1-6aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl,and alkynyl groups employed in the invention contain 1-4 carbon atoms.Illustrative aliphatic groups thus include, but are not limited to, forexample, methyl, ethyl, n-propyl, isopropyl, cyclopropyl,—CH₂-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl,tert-butyl, cyclobutyl, —CH₂-cyclobutyl, n-pentyl, sec-pentyl,isopentyl, tert-pentyl, cyclopentyl, —CH₂-cyclopentyl, n-hexyl,sec-hexyl, cyclohexyl, —CH₂-cyclohexyl moieties and the like, whichagain, may bear one or more substituents. Alkenyl groups include, butare not limited to, for example, ethenyl, propenyl, butenyl,1-methyl-2-buten-1-yl, and the like. Representative alkynyl groupsinclude, but are not limited to, ethynyl, 2-propynyl (propargyl),1-propynyl, and the like.

“Alkyl” refers to a radical of a straight-chain or branched saturatedhydrocarbon group having from 1 to 20 carbon atoms (“C₁₋₂₀ alkyl”). Insome embodiments, an alkyl group has 1 to 10 carbon atoms (“C₁₋₁₀alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms(“C₁₋₉ alkyl”). In some embodiments, an alkyl group has 1 to 8 carbonatoms (“C₁₋₈ alkyl”). In some embodiments, an alkyl group has 1 to 7carbon atoms (“C₁₋₇ alkyl”). In some embodiments, an alkyl group has 1to 6 carbon atoms (“C₁₋₆ alkyl”). In some embodiments, an alkyl grouphas 1 to 5 carbon atoms (“C₁₋₅ alkyl”). In some embodiments, an alkylgroup has 1 to 4 carbon atoms (“C₁₋₄ alkyl”). In some embodiments, analkyl group has 1 to 3 carbon atoms (“C₁₋₃ alkyl”). In some embodiments,an alkyl group has 1 to 2 carbon atoms (“C₁₋₂ alkyl”). In someembodiments, an alkyl group has 1 carbon atom (“C₁ alkyl”). In someembodiments, an alkyl group has 2 to 6 carbon atoms (“C₂₋₆ alkyl”).Examples of C₁₋₆ alkyl groups include methyl (C₁), ethyl (C₂), n-propyl(C₃), isopropyl (C₃), n-butyl (C₄), tert-butyl (C₄), sec-butyl (C₄),iso-butyl (C₄), n-pentyl (C₅), 3-pentanyl (C₅), amyl (C₅), neopentyl(C₅), 3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n-hexyl (C₆).Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈)and the like. Unless otherwise specified, each instance of an alkylgroup is independently optionally substituted, i.e., unsubstituted (an“unsubstituted alkyl”) or substituted (a “substituted alkyl”) with oneor more substituents (e.g., halogen, such as F). In certain embodiments,the alkyl group is unsubstituted C₁₋₁₀ alkyl (e.g., CH₃ (Me),unsubstituted ethyl (Et), unsubstituted propyl (Pr, e.g., unsubstitutedn-propyl (n-Pr), unsubstituted isopropyl (i-Pr)), unsubstituted butyl(Bu, e.g., unsubstituted n-butyl (n-Bu), unsubstituted tert-butyl(tert-Bu or t-Bu), unsubstituted sec-butyl (sec-Bu), unsubstitutedisobutyl (i-Bu)). In certain embodiments, the alkyl group is substitutedC₁₋₁₀ alkyl (such as substituted C₁₋₆ alkyl, e.g., CF₃, Bn).

“Alkenyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon double bonds, and no triple bonds (“C₂₋₂₀ alkenyl”). Insome embodiments, an alkenyl group has 2 to 10 carbon atoms (“C₂₋₁₀alkenyl”). In some embodiments, an alkenyl group has 2 to 9 carbon atoms(“C₂₋₉ alkenyl”). In some embodiments, an alkenyl group has 2 to 8carbon atoms (“C₂₋₈ alkenyl”). In some embodiments, an alkenyl group has2 to 7 carbon atoms (“C₂₋₇ alkenyl”). In some embodiments, an alkenylgroup has 2 to 6 carbon atoms (“C₂₋₆ alkenyl”). In some embodiments, analkenyl group has 2 to 5 carbon atoms (“C₂₋₅ alkenyl”). In someembodiments, an alkenyl group has 2 to 4 carbon atoms (“C₂₋₄ alkenyl”).In some embodiments, an alkenyl group has 2 to 3 carbon atoms (“C₂₋₃alkenyl”). In some embodiments, an alkenyl group has 2 carbon atoms (“C₂alkenyl”). The one or more carbon carbon double bonds can be internal(such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples ofC₂₋₄ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl(C₃), 1 butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like.Examples of C₂₋₆ alkenyl groups include the aforementioned C₂₋₄ alkenylgroups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and thelike. Additional examples of alkenyl include heptenyl (C₇), octenyl(C₈), octatrienyl (C₈), and the like. Unless otherwise specified, eachinstance of an alkenyl group is independently optionally substituted,i.e., unsubstituted (an “unsubstituted alkenyl”) or substituted (a“substituted alkenyl”) with one or more substituents. In certainembodiments, the alkenyl group is unsubstituted C₂₋₁₀ alkenyl. Incertain embodiments, the alkenyl group is substituted C₂₋₁₀ alkenyl. Inan alkenyl group, a C═C double bond for which the stereochemistry is notspecified (e.g., —CH═CHCH₃ or

may be an (E)- or (Z)-double bond.

“Alkynyl” refers to a radical of a straight-chain or branchedhydrocarbon group having from 2 to 20 carbon atoms, one or morecarbon-carbon triple bonds, and optionally one or more double bonds(“C₂₋₂₀ alkynyl”). In some embodiments, an alkynyl group has 2 to 10carbon atoms (“C₂₋₁₀ alkynyl”). In some embodiments, an alkynyl grouphas 2 to 9 carbon atoms (“C₂₋₉ alkynyl”). In some embodiments, analkynyl group has 2 to 8 carbon atoms (“C₂₋₈ alkynyl”). In someembodiments, an alkynyl group has 2 to 7 carbon atoms (“C₂₋₇ alkynyl”).In some embodiments, an alkynyl group has 2 to 6 carbon atoms (“C₂₋₆alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms(“C₂₋₅ alkynyl”). In some embodiments, an alkynyl group has 2 to 4carbon atoms (“C₂₋₄ alkynyl”). In some embodiments, an alkynyl group has2 to 3 carbon atoms (“C₂₋₃ alkynyl”). In some embodiments, an alkynylgroup has 2 carbon atoms (“C₂ alkynyl”). The one or more carbon-carbontriple bonds can be internal (such as in 2-butynyl) or terminal (such asin 1-butynyl). Examples of C₂₋₄ alkynyl groups include, withoutlimitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl(C₄), 2-butynyl (C₄), and the like. Examples of C₂₋₆ alkenyl groupsinclude the aforementioned C₂₋₄ alkynyl groups as well as pentynyl (C₅),hexynyl (C₆), and the like. Additional examples of alkynyl includeheptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified,each instance of an alkynyl group is independently optionallysubstituted, i.e., unsubstituted (an “unsubstituted alkynyl”) orsubstituted (a “substituted alkynyl”) with one or more substituents. Incertain embodiments, the alkynyl group is unsubstituted C₂₋₁₀ alkynyl.In certain embodiments, the alkynyl group is substituted C₂₋₁₀ alkynyl.

“Carbocyclyl” or “carbocyclic” refers to a radical of a non-aromaticcyclic hydrocarbon group having from 3 to 10 ring carbon atoms (“C₃₋₁₀carbocyclyl”) and zero heteroatoms in the non-aromatic ring system. Insome embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms(“C₃₋₈ carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to6 ring carbon atoms (“C₃₋₆ carbocyclyl”). In some embodiments, acarbocyclyl group has 3 to 6 ring carbon atoms (“C₃₋₆ carbocyclyl”). Insome embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms(“C₅₋₁₀ carbocyclyl”). Exemplary C₃₋₆ carbocyclyl groups include,without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl(C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅),cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like.Exemplary C₃₋₈ carbocyclyl groups include, without limitation, theaforementioned C₃₋₆ carbocyclyl groups as well as cycloheptyl (C₇),cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇),cyclooctyl (C₈), cyclooctenyl (C₈), bicyclo[2.2.1]heptanyl (C₇),bicyclo[2.2.2]octanyl (C₈), and the like. Exemplary C₃₋₁₀ carbocyclylgroups include, without limitation, the aforementioned C₃₋₈ carbocyclylgroups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀),cyclodecenyl (C₁₀), octahydro-1H-indenyl (C₉), decahydronaphthalenyl(C₁₀), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examplesillustrate, in certain embodiments, the carbocyclyl group is eithermonocyclic (“monocyclic carbocyclyl”) or contain a fused, bridged orspiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) andcan be saturated or can be partially unsaturated. “Carbocyclyl” alsoincludes ring systems wherein the carbocyclic ring, as defined above, isfused with one or more aryl or heteroaryl groups wherein the point ofattachment is on the carbocyclic ring, and in such instances, the numberof carbons continue to designate the number of carbons in thecarbocyclic ring system. Unless otherwise specified, each instance of acarbocyclyl group is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted carbocyclyl”) or substituted (a“substituted carbocyclyl”) with one or more substituents. In certainembodiments, the carbocyclyl group is unsubstituted C₃₋₁₀ carbocyclyl.In certain embodiments, the carbocyclyl group is substituted C₃₋₁₀carbocyclyl.

In some embodiments, “carbocyclyl” is a monocyclic, saturatedcarbocyclyl group having from 3 to 10 ring carbon atoms (“C₃₋₁₀cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ringcarbon atoms (“C₃₋₈ cycloalkyl”). In some embodiments, a cycloalkylgroup has 3 to 6 ring carbon atoms (“C₃₋₆ cycloalkyl”). In someembodiments, a cycloalkyl group has 5 to 6 ring carbon atoms (“C₅₋₆cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 10 ringcarbon atoms (“C₅₋₁₀ cycloalkyl”). Examples of C₅₋₆ cycloalkyl groupsinclude cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃₋₆cycloalkyl groups include the aforementioned C₅₋₆ cycloalkyl groups aswell as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃₋₈cycloalkyl groups include the aforementioned C₃₋₆ cycloalkyl groups aswell as cycloheptyl (C₇) and cyclooctyl (C₈). Unless otherwisespecified, each instance of a cycloalkyl group is independentlyunsubstituted (an “unsubstituted cycloalkyl”) or substituted (a“substituted cycloalkyl”) with one or more substituents. In certainembodiments, the cycloalkyl group is unsubstituted C₃₋₁₀ cycloalkyl. Incertain embodiments, the cycloalkyl group is substituted C₃₋₁₀cycloalkyl.

“Heterocyclyl” or “heterocyclic” refers to a radical of a 3- to10-membered non aromatic ring system having ring carbon atoms and 1 to 4ring heteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“3-10 memberedheterocyclyl”). In heterocyclyl groups that contain one or more nitrogenatoms, the point of attachment can be a carbon or nitrogen atom, asvalency permits. A heterocyclyl group can either be monocyclic(“monocyclic heterocyclyl”) or a fused, bridged, or spiro ring system,such as a bicyclic system (“bicyclic heterocyclyl”), and can besaturated or can be partially unsaturated. Heterocyclyl bicyclic ringsystems can include one or more heteroatoms in one or both rings.“Heterocyclyl” also includes ring systems wherein the heterocyclic ring,as defined above, is fused with one or more carbocyclyl groups whereinthe point of attachment is either on the carbocyclyl or heterocyclicring, or ring systems wherein the heterocyclic ring, as defined above,is fused with one or more aryl or heteroaryl groups, wherein the pointof attachment is on the heterocyclic ring, and in such instances, thenumber of ring members continue to designate the number of ring membersin the heterocyclic ring system. Unless otherwise specified, eachinstance of heterocyclyl is independently optionally substituted, i.e.,unsubstituted (an “unsubstituted heterocyclyl”) or substituted (a“substituted heterocyclyl”) with one or more substituents. In certainembodiments, the heterocyclyl group is unsubstituted 3-10 memberedheterocyclyl. In certain embodiments, the heterocyclyl group issubstituted 3-10 membered heterocyclyl.

In some embodiments, a heterocyclyl group is a 5-10 memberednon-aromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, sulfur, boron, phosphorus, and silicon (“5-10 memberedheterocyclyl”). In some embodiments, a heterocyclyl group is a 5-8membered nonaromatic ring system having ring carbon atoms and 1-4 ringheteroatoms, wherein each heteroatom is independently selected fromnitrogen, oxygen, and sulfur (“5-8 membered heterocyclyl”). In someembodiments, a heterocyclyl group is a 5-6 membered non-aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms, wherein eachheteroatom is independently selected from nitrogen, oxygen, and sulfur(“5-6 membered heterocyclyl”). In some embodiments, the 5-6 memberedheterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen,and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2ring heteroatoms selected from nitrogen, oxygen, and sulfur. In someembodiments, the 5-6 membered heterocyclyl has one ring heteroatomselected from nitrogen, oxygen, and sulfur.

Exemplary 3-membered heterocyclyl groups containing one heteroatominclude, without limitation, azirdinyl, oxiranyl, and thiiranyl.Exemplary 4-membered heterocyclyl groups containing one heteroatominclude, without limitation, azetidinyl, oxetanyl and thietanyl.Exemplary 5-membered heterocyclyl groups containing one heteroatominclude, without limitation, tetrahydrofuranyl, dihydrofuranyl,tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl,and pyrrolyl-2,5-dione. Exemplary 5 membered heterocyclyl groupscontaining two heteroatoms include, without limitation, dioxolanyl,oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-memberedheterocyclyl groups containing three heteroatoms include, withoutlimitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary6-membered heterocyclyl groups containing one heteroatom include,without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl,and thianyl. Exemplary 6-membered heterocyclyl groups containing twoheteroatoms include, without limitation, piperazinyl, morpholinyl,dithianyl, and dioxanyl. Exemplary 6 membered heterocyclyl groupscontaining two heteroatoms include, without limitation, triazinanyl.Exemplary 7-membered heterocyclyl groups containing one heteroatominclude, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary8-membered heterocyclyl groups containing one heteroatom include,without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary5-membered heterocyclyl groups fused to a C₆ aryl ring (also referred toherein as a 5,6-bicyclic heterocyclic ring) include, without limitation,indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groupsfused to an aryl ring (also referred to herein as a 6,6-bicyclicheterocyclic ring) include, without limitation, tetrahydroquinolinyl,tetrahydroisoquinolinyl, and the like.

“Aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclicor tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 pielectrons shared in a cyclic array) having 6-14 ring carbon atoms andzero heteroatoms provided in the aromatic ring system (“C₆₋₁₄ aryl”). Insome embodiments, an aryl group has six ring carbon atoms (“C₆ aryl”;e.g., phenyl). In some embodiments, an aryl group has ten ring carbonatoms (“C₁₀ aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). Insome embodiments, an aryl group has fourteen ring carbon atoms (“C₁₄aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein thearyl ring, as defined above, is fused with one or more carbocyclyl orheterocyclyl groups wherein the radical or point of attachment is on thearyl ring, and in such instances, the number of carbon atoms continue todesignate the number of carbon atoms in the aryl ring system. Unlessotherwise specified, each instance of an aryl group is independentlyoptionally substituted, i.e., unsubstituted (an “unsubstituted aryl”) orsubstituted (a “substituted aryl”) with one or more substituents. Incertain embodiments, the aryl group is unsubstituted C₆₋₁₄ aryl. Incertain embodiments, the aryl group is substituted C₆₋₁₄ aryl.

“Aralkyl” is a subset of alkyl and aryl and refers to an optionallysubstituted alkyl group substituted by an optionally substituted arylgroup. In certain embodiments, the aralkyl is optionally substitutedbenzyl. In certain embodiments, the aralkyl is benzyl. In certainembodiments, the aralkyl is optionally substituted phenethyl. In certainembodiments, the aralkyl is phenethyl.

“Heteroaryl” refers to a radical of a 5-10 membered monocyclic orbicyclic 4n+2 aromatic ring system (e.g., having 6 or 10 pi electronsshared in a cyclic array) having ring carbon atoms and 1-4 ringheteroatoms provided in the aromatic ring system, wherein eachheteroatom is independently selected from nitrogen, oxygen and sulfur(“5-10 membered heteroaryl”). In heteroaryl groups that contain one ormore nitrogen atoms, the point of attachment can be a carbon or nitrogenatom, as valency permits. Heteroaryl bicyclic ring systems can includeone or more heteroatoms in one or both rings. “Heteroaryl” includes ringsystems wherein the heteroaryl ring, as defined above, is fused with oneor more carbocyclyl or heterocyclyl groups wherein the point ofattachment is on the heteroaryl ring, and in such instances, the numberof ring members continue to designate the number of ring members in theheteroaryl ring system. “Heteroaryl” also includes ring systems whereinthe heteroaryl ring, as defined above, is fused with one or more arylgroups wherein the point of attachment is either on the aryl orheteroaryl ring, and in such instances, the number of ring membersdesignates the number of ring members in the fused (aryl/heteroaryl)ring system. Bicyclic heteroaryl groups wherein one ring does notcontain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and thelike) the point of attachment can be on either ring, i.e., either thering bearing a heteroatom (e.g., 2-indolyl) or the ring that does notcontain a heteroatom (e.g., 5 indolyl).

In some embodiments, a heteroaryl group is a 5-10 membered aromatic ringsystem having ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-10 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-8 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-8 membered heteroaryl”). In someembodiments, a heteroaryl group is a 5-6 membered aromatic ring systemhaving ring carbon atoms and 1-4 ring heteroatoms provided in thearomatic ring system, wherein each heteroatom is independently selectedfrom nitrogen, oxygen, and sulfur (“5-6 membered heteroaryl”). In someembodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatomsselected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen,oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unlessotherwise specified, each instance of a heteroaryl group isindependently optionally substituted, i.e., unsubstituted (an“unsubstituted heteroaryl”) or substituted (a “substituted heteroaryl”)with one or more substituents. In certain embodiments, the heteroarylgroup is unsubstituted 5-14 membered heteroaryl. In certain embodiments,the heteroaryl group is substituted 5-14 membered heteroaryl.

Exemplary 5-membered heteroaryl groups containing one heteroatominclude, without limitation, pyrrolyl, furanyl, and thiophenyl.Exemplary 5-membered heteroaryl groups containing two heteroatomsinclude, without limitation, imidazolyl, pyrazolyl, oxazolyl,isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroarylgroups containing three heteroatoms include, without limitation,triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-memberedheteroaryl groups containing four heteroatoms include, withoutlimitation, tetrazolyl. Exemplary 6-membered heteroaryl groupscontaining one heteroatom include, without limitation, pyridinyl.Exemplary 6-membered heteroaryl groups containing two heteroatomsinclude, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.Exemplary 6-membered heteroaryl groups containing three or fourheteroatoms include, without limitation, triazinyl and tetrazinyl,respectively. Exemplary 7-membered heteroaryl groups containing oneheteroatom include, without limitation, azepinyl, oxepinyl, andthiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, withoutlimitation, indolyl, isoindolyl, indazolyl, benzotriazolyl,benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl,benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl,benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, andpurinyl. Exemplary 6,6-bicyclic heteroaryl groups include, withoutlimitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.

“Heteroaralkyl” is a subset of alkyl and heteroaryl and refers to anoptionally substituted alkyl group substituted by an optionallysubstituted heteroaryl group.

“Unsaturated” or “partially unsaturated” refers to a group that includesat least one double or triple bond. A “partially unsaturated” ringsystem is further intended to encompass rings having multiple sites ofunsaturation, but is not intended to include aromatic groups (e.g., arylor heteroaryl groups) as herein defined. Likewise, “saturated” refers toa group that does not contain a double or triple bond, i.e., containsall single bonds.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups, which are divalent bridging groups, are further referred tousing the suffix ene, e.g., alkylene, alkenylene, alkynylene,carbocyclylene, heterocyclylene, arylene, and heteroarylene.

An atom, moiety, or group described herein may be unsubstituted orsubstituted, as valency permits, unless otherwise provided expressly.The term “optionally substituted” refers to substituted orunsubstituted.

Alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylgroups are optionally substituted (e.g., “substituted” or“unsubstituted” alkyl, “substituted” or “unsubstituted” alkenyl,“substituted” or “unsubstituted” alkynyl, “substituted” or“unsubstituted” carbocyclyl, “substituted” or “unsubstituted”heterocyclyl, “substituted” or “unsubstituted” aryl or “substituted” or“unsubstituted” heteroaryl group). In general, the term “substituted”,whether preceded by the term “optionally” or not, means that at leastone hydrogen present on a group (e.g., a carbon or nitrogen atom) isreplaced with a permissible substituent, e.g., a substituent which uponsubstitution results in a stable compound, e.g., a compound which doesnot spontaneously undergo transformation such as by rearrangement,cyclization, elimination, or other reaction. Unless otherwise indicated,a “substituted” group has a substituent at one or more substitutablepositions of the group, and when more than one position in any givenstructure is substituted, the substituent is either the same ordifferent at each position. The term “substituted” is contemplated toinclude substitution with all permissible substituents of organiccompounds, any of the substituents described herein that results in theformation of a stable compound. The present invention contemplates anyand all such combinations in order to arrive at a stable compound. Forpurposes of this invention, heteroatoms such as nitrogen may havehydrogen substituents and/or any suitable substituent as describedherein which satisfy the valencies of the heteroatoms and results in theformation of a stable moiety. In certain embodiments, the substituent isa carbon atom substituent. In certain embodiments, the substituent is anitrogen atom substituent. In certain embodiments, the substituent is anoxygen atom substituent. In certain embodiments, the substituent is asulfur atom substituent.

Exemplary carbon atom substituents include, but are not limited to,halogen, —CN, —NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(aa), —ON(R^(bb))₂,—N(R^(bb))₂, —N(R^(bb))₃ ⁺X⁻, —N(OR^(cc))R^(bb), —SH, —SR^(aa),—SSR^(cc), —C(═O)R^(aa), —CO₂H, —CHO, —C(OR^(cc))₂, —CO₂R^(aa),—OC(═O)R^(aa), —OCO₂R^(aa), —C(═O)N(R^(bb))₂, —OC(═O)N(R^(bb))₂,—NR^(bb)C(═O)R^(aa), —NR^(bb)CO₂R^(aa), —NR^(bb)C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —OC(═NR^(bb))R^(aa),—OC(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —OC(═NR^(bb))N(R^(bb))₂,—NR^(bb)C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—NR^(bb)SO₂R^(aa), —SO₂N(R^(bb))₂, —SO₂R^(aa), —SO₂OR^(aa), —OSO₂R^(aa),—S(═O)R^(aa), —OS(═O)R^(aa), —Si(R^(aa))₃,—OSi(R^(aa))₃—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), —C(═S)SR^(aa),—SC(═S)SR^(aa), —SC(═O)SR^(aa), —OC(═O)SR^(aa), —SC(═O)OR^(aa),—SC(═O)R^(aa), —P(═O)₂R^(aa), —OP(═O)₂R^(aa), —P(═O)(R^(aa))₂,—OP(═O)(R^(aa))₂, —OP(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂,—OP(═O)₂N(R^(bb))₂, —P(═O)(NR^(bb))₂, —OP(═O)(NR^(bb))₂,—NR^(bb)P(═O)(OR^(cc))₂, —NR^(bb)P(═O)(NR^(bb))₂, —P(R^(cc))₂,—P(R^(cc))₃, —OP(R^(cc))₂, —OP(R^(cc))₃, —B(R^(aa))₂, —B(OR^(cc))₂,—BR^(aa)(OR^(cc)), C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups; or two geminalhydrogens on a carbon atom are replaced with the group ═O, ═S,═NN(R^(bb))₂, ═NNR^(bb)C(═O)R^(aa), ═NNR^(bb)C(═O)OR^(aa),═NNR^(bb)S(═O)₂R^(aa), ═NR^(bb), or ═NOR^(cc);

each instance of R^(aa) is, independently, selected from C₁₋₁₀ alkyl,C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀ carbocyclyl,3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 membered heteroaryl, ortwo R^(aa) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(bb) is, independently, selected from hydrogen, —OH,—OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂,—SO₂R^(cc), —SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc),—C(═S)SR^(cc), —P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂,—P(═O)(NR^(cc))₂, C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀alkynyl, C₃₋₁₀ carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and5-14 membered heteroaryl, or two R^(bb) groups are joined to form a 3-14membered heterocyclyl or 5-14 membered heteroaryl ring, wherein eachalkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroarylis independently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(cc) is, independently, selected from hydrogen, C₁₋₁₀alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups are joined to form a 3-14 memberedheterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl,alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl isindependently substituted with 0, 1, 2, 3, 4, or 5 R^(dd) groups;

each instance of R^(dd) is, independently, selected from halogen, —CN,—NO₂, —N₃, —SO₂H, —SO₃H, —OH, —OR^(ee), —ON(R^(ff))₂, —N(R^(ff))₂,—N(R^(ff))₃ ⁺X⁻, —N(OR^(ee))R^(ff), —SH, —SR^(ee), —SSR^(ee),—C(═O)R^(ee), —CO₂H, —CO₂R^(ee), —OC(═O)R^(ee), —OCO₂R^(ee),—C(═O)N(R^(ff))₂, —OC(═O)N(R^(ff))₂, —NR^(ff)C(═O)R^(ee),—NR^(ff)CO₂R^(ee), —NR^(ff)C(═O)N(R^(ff))₂, —C(═NR^(ff))OR^(ee),—OC(═NR^(ff))R^(ee), —OC(═NR^(ff))OR^(ee), —C(═NR^(ff))N(R^(ff))₂,—OC(═NR^(ff))N(R^(ff))₂, —NR^(ff)C(═NR^(ff))N(R^(ff))₂,—NR^(ff)SO₂R^(ee), —SO₂N(R^(ff))₂, —SO₂R^(ee), —SO₂OR^(ee), —OSO₂R^(ee),—S(═O)R^(ee), —Si(R^(ee))₃, —OSi(R^(ee))₃, —C(═S)N(R^(ff))₂,—C(═O)SR^(ee), —C(═S)SR^(ee), —SC(═S)SR^(ee), —P(═O)₂R^(ee),—P(═O)(R^(ee))₂, —OP(═O)(R^(ee))₂, —OP(═O)(OR^(ee))₂, C₁₋₆ alkyl, C₁₋₆perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, 3-10membered heterocyclyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups, or two geminal R^(dd) substituents can be joined to form ═O or═S;

each instance of R^(ee) is, independently, selected from C₁₋₆ alkyl,C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl, C₆₋₁₀aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, whereineach alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, andheteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R^(gg)groups;

each instance of R^(ff) is, independently, selected from hydrogen, C₁₋₆alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₁₀ carbocyclyl,3-10 membered heterocyclyl, C₆₋₁₀ aryl and 5-10 membered heteroaryl, ortwo R^(ff) groups are joined to form a 3-14 membered heterocyclyl or5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl,carbocyclyl, heterocyclyl, aryl, and heteroaryl is independentlysubstituted with 0, 1, 2, 3, 4, or 5 R^(gg) groups; and

each instance of R^(gg) is, independently, halogen, —CN, —NO₂, —N₃,—SO₂H, —SO₃H, —OH, —OC₁₋₆ alkyl, —ON(C₁₋₆ alkyl)₂, —N(C₁₋₆ alkyl)₂,—N(C₁₋₆ alkyl)₃ ⁺X⁻, —NH(C₁₋₆ alkyl)₂ ⁺X⁻, —NH₂(C₁₋₆ alkyl)⁺X⁻, —NH₃⁺X⁻, —N(OC₁₋₆ alkyl)(C₁₋₆ alkyl), —N(OH)(C₁₋₆ alkyl), —NH(OH), —SH,—SC₁₋₆ alkyl, —SS(C₁₋₆ alkyl), —C(═O)(C₁₋₆ alkyl), —CO₂H, —CO₂(C₁₋₆alkyl), —OC(═O)(C₁₋₆ alkyl), —OCO₂(C₁₋₆ alkyl), —C(═O)NH₂, —C(═O)N(C₁₋₆alkyl)₂, —OC(═O)NH(C₁₋₆ alkyl), —NHC(═O)(C₁₋₆ alkyl), —N(C₁₋₆alkyl)C(═O)(C₁₋₆ alkyl), —NHCO₂(C₁₋₆ alkyl), —NHC(═O)N(C₁₋₆ alkyl)₂,—NHC(═O)NH(C₁₋₆ alkyl), —NHC(═O)NH₂, —C(═NH)O(C₁₋₆ alkyl), —OC(═NH)(C₁₋₆alkyl), —OC(═NH)OC₁₋₆ alkyl, —C(═NH)N(C₁₋₆ alkyl)₂, —C(═NH)NH(C₁₋₆alkyl), —C(═NH)NH₂, —OC(═NH)N(C₁₋₆ alkyl)₂, —OC(NH)NH(C₁₋₆ alkyl),—OC(NH)NH₂, —NHC(NH)N(C₁₋₆ alkyl)₂, —NHC(═NH)NH₂, —NHSO₂(C₁₋₆ alkyl),—SO₂N(C₁₋₆ alkyl)₂, —SO₂NH(C₁₋₆ alkyl), —SO₂NH₂, —SO₂C₁₋₆ alkyl,—SO₂OC₁₋₆ alkyl, —OSO₂C₁₋₆ alkyl, —SOC₁₋₆ alkyl, —Si(C₁₋₆ alkyl)₃,—OSi(C₁₋₆ alkyl)₃-C(═S)N(C₁₋₆ alkyl)₂, C(═S)NH(C₁₋₆ alkyl), C(═S)NH₂,—C(═O)S(C₁₋₆ alkyl), —C(═S)SC₁₋₆ alkyl, —SC(═S)SC₁₋₆ alkyl, —P(═O)₂(C₁₋₆alkyl), —P(═O)(C₁₋₆ alkyl)₂, —OP(═O)(C₁₋₆ alkyl)₂, —OP(═O)(OC₁₋₆alkyl)₂, C₁₋₆ alkyl, C₁₋₆ perhaloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,C₃₋₁₀ carbocyclyl, C₆₋₁₀ aryl, 3-10 membered heterocyclyl, 5-10 memberedheteroaryl; or two geminal R^(gg) substituents can be joined to form ═Oor ═S; wherein X⁻ is a counterion.

A “counterion” or “anionic counterion” is a negatively charged groupassociated with a cationic quaternary amino group in order to maintainelectronic neutrality. Exemplary counterions include halide ions (e.g.,F⁻, Cl⁻, Br⁻, I⁻), NO₃ ⁻, ClO₄ ⁻, OH⁻, H₂PO₄ ⁻, HSO₄ ⁻, sulfonate ions(e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate,benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate,naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonicacid-2-sulfonate, and the like), BF₄ ⁻, PF₄ ⁻, PF₆ ⁻, AsF₆ ⁻, SbF₆ ⁻,B[3,5-(CF₃)₂C₆H₃]₄]⁻, BPh₄ ⁻, Al(OC(CF₃)₃)₄ ⁻, carborane anions (e.g.,CB₁₁H₁₂ ⁻ or (HCB₁₁Me₅Br₆)⁻), and carboxylate ions (e.g., acetate,ethanoate, propanoate, benzoate, glycerate, lactate, tartrate,glycolate, and the like).

“Halo” or “halogen” refers to fluorine (fluoro, —F), chlorine (chloro,—Cl), bromine (bromo, —Br), or iodine (iodo, —I).

“Acyl” refers to a moiety selected from the group consisting of—C(═O)R^(aa), —CHO, —CO₂R^(aa), —C(═NR^(bb))₂, —C(═NR^(bb))R^(aa),—C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂, —C(═O)NR^(bb)SO₂R^(aa),—C(═S)N(R^(bb))₂, —C(═O)SR^(aa), or —C(═S)SR^(aa), wherein R^(aa) andR^(bb) are as defined herein.

Nitrogen atoms can be substituted or unsubstituted as valency permits,and include primary, secondary, tertiary, and quaternary nitrogen atoms.Exemplary nitrogen atom substituents include, but are not limited to,hydrogen, —OH, —OR^(aa), —N(R^(cc))₂, —CN, —C(═O)R^(aa),—C(═O)N(R^(cc))₂, —CO₂R^(aa), —SO₂R^(aa), —C(═NR^(bb))R^(aa),—C(═NR^(cc))OR^(aa), —C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc),—SO₂OR^(cc), —SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc),—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)₂N(R^(cc))₂, —P(═O)(NR^(cc))₂,C₁₋₁₀ alkyl, C₁₋₁₀ perhaloalkyl, C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl, or two R^(cc) groups attached to a nitrogen atom are joinedto form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring,wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl,and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5R^(dd) groups, and wherein R^(aa), R^(bb), R^(cc), and R^(dd) are asdefined above.

In certain embodiments, the substituent present on a nitrogen atom is anitrogen protecting group (also referred to as an amino protectinggroup). Nitrogen protecting groups include, but are not limited to, —OH,—OR^(aa), —N(R^(cc))₂, —C(═O)R^(aa), —C(═O)N(R^(cc))₂, —CO₂R^(aa),—SO₂R^(aa), —C(═NR^(cc))R^(aa), —C(═NR^(cc))OR^(aa),—C(═NR^(cc))N(R^(cc))₂, —SO₂N(R^(cc))₂, —SO₂R^(cc), —SO₂OR^(cc),—SOR^(aa), —C(═S)N(R^(cc))₂, —C(═O)SR^(cc), —C(═S)SR^(cc), C₁₋₁₀ alkyl(e.g., aralkyl, heteroaralkyl), C₂₋₁₀ alkenyl, C₂₋₁₀ alkynyl, C₃₋₁₀carbocyclyl, 3-14 membered heterocyclyl, C₆₋₁₄ aryl, and 5-14 memberedheteroaryl groups, wherein each alkyl, alkenyl, alkynyl, carbocyclyl,heterocyclyl, aralkyl, aryl, and heteroaryl is independently substitutedwith 0, 1, 2, 3, 4, or 5 R^(dd) groups, and wherein R^(aa), R^(bb),R^(cc) and R^(dd) are as defined herein. Nitrogen protecting groups arewell known in the art and include those described in detail inProtecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts,3^(rd) edition, John Wiley & Sons, 1999, incorporated herein byreference.

For example, nitrogen protecting groups such as amide groups (e.g.,—C(═O)R^(aa)) include, but are not limited to, formamide, acetamide,chloroacetamide, trichloroacetamide, trifluoroacetamide,phenylacetamide, 3-phenylpropanamide, picolinamide,3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide,p-phenylbenzamide, o-nitophenylacetamide, o-nitrophenoxyacetamide,acetoacetamide, (N′-dithiobenzyloxyacylamino)acetamide,3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,2-methyl-2-(o-nitrophenoxy)propanamide,2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethioninederivative, o-nitrobenzamide, and o-(benzoyloxymethyl)benzamide.

Nitrogen protecting groups such as carbamate groups (e.g.,—C(═O)OR^(aa)) include, but are not limited to, methyl carbamate, ethylcarbamante, 9-fluorenylmethyl carbamate (Fmoc),9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethylcarbamate,2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methylcarbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate(Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethylcarbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate,1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC),1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC),1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethylcarbamate, t-butyl carbamate (BOC or Boc), 1-adamantyl carbamate (Adoc),vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallylcarbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate(Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithiocarbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzylcarbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate,2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate,2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methylcarbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc),2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate(Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc),1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate,p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate,2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenylcarbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate,3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methylcarbamate, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzylcarbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentylcarbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate,2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzylcarbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate,isobutyl carbamate, isonicotinyl carbamate,p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate,1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate,1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate,p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate,4-(trimethylammonium)benzyl carbamate, and 2,4,6-trimethylbenzylcarbamate.

Nitrogen protecting groups such as sulfonamide groups (e.g.,—S(═O)₂R^(aa)) include, but are not limited to, p-toluenesulfonamide(Ts), benzenesulfonamide, 2,3,6,-trimethyl-4-methoxybenzenesulfonamide(Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb),2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide(Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide(Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide,4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide.

Other nitrogen protecting groups include, but are not limited to,phenothiazinyl-(10)-acyl derivative, N′-p-toluenesulfonylaminoacylderivative, N′-phenylaminothioacyl derivative, N-benzoylphenylalanylderivative, N-acetylmethionine derivative,4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts),N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole,N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE),5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine,N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammoniumsalts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),N-9-phenylfluorenylamine (PhF),N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm),N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine,N-benzylideneamine, N-p-methoxybenzylideneamine,N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine,N-p-nitrobenzylideneamine, N-salicylideneamine,N-5-chlorosalicylideneamine,N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine,N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,N-borane derivative, N-diphenylborinic acid derivative,N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper chelate,N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide,diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt),diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzylphosphoramidate, diphenyl phosphoramidate, benzenesulfenamide,o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide,pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys). Incertain embodiments, a nitrogen protecting group described herein is Bn,Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts.

Exemplary oxygen atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃,—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and—P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein. In certain embodiments, the oxygen atom substituent present onan oxygen atom is an oxygen protecting group (also referred to as ahydroxyl protecting group). Oxygen protecting groups are well known inthe art and include those described in detail in Protecting Groups inOrganic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, JohnWiley & Sons, 1999, incorporated herein by reference. Exemplary oxygenprotecting groups include, but are not limited to, methyl,t-butyloxycarbonyl (BOC or Boc), methoxylmethyl (MOM), methylthiomethyl(MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM),benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM),(4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl,4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM),2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl,2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP),3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl,4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl,4-methoxytetrahydrothiopyranyl S,S-dioxide,1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP),1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl,t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl,benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl,p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl,p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido,diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl,triphenylmethyl, α-naphthyldiphenylmethyl,p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl,tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl,4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl,4,4′,4″-tris(levulinoyloxyphenyl)methyl,4,4′,4″-tris(benzoyloxyphenyl)methyl,3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl,1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl,9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,1,3-benzodisulfuran-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl(TMS), triethylsilyl (TES), triisopropylsilyl (TIPS),dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS),dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl(TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate,benzoylformate, acetate, chloroacetate, dichloroacetate,trichloroacetate, trifluoroacetate, methoxyacetate,triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate,3-phenylpropionate, 4-oxopentanoate (levulinate),4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate,adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate,2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate(TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec),2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutylcarbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkylp-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzylcarbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzylcarbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate,4-ethoxy-1-napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate,4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,2,6-dichloro-4-methylphenoxyacetate,2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate,o-(methoxyacyl)benzoate, α-naphthoate, nitrate, alkylN,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate(Ts). In certain embodiments, an oxygen protecting group describedherein is silyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn,allyl, acetyl, pivaloyl, or benzoyl.

Exemplary sulfur atom substituents include, but are not limited to,—R^(aa), —C(═O)SR^(aa), —C(═O)R^(aa), —CO₂R^(aa), —C(═O)N(R^(bb))₂,—C(═NR^(bb))R^(aa), —C(═NR^(bb))OR^(aa), —C(═NR^(bb))N(R^(bb))₂,—S(═O)R^(aa), —SO₂R^(aa), —Si(R^(aa))₃, —P(R^(cc))₂, —P(R^(cc))₃,—P(═O)₂R^(aa), —P(═O)(R^(aa))₂, —P(═O)(OR^(cc))₂, —P(═O)₂N(R^(bb))₂, and—P(═O)(NR^(bb))₂, wherein R^(aa), R^(bb), and R^(cc) are as definedherein. In certain embodiments, the sulfur atom substituent present on asulfur atom is a sulfur protecting group (also referred to as a thiolprotecting group). Sulfur protecting groups are well known in the artand include those described in detail in Protecting Groups in OrganicSynthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley &Sons, 1999, incorporated herein by reference. In certain embodiments, asulfur protecting group described herein is acetamidomethyl, t-Bu,3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl.

The invention is not intended to be limited in any manner by the aboveexemplary listing of substituents.

Other Definitions

The following definitions are more general terms used throughout thepresent application.

The term “pharmaceutically acceptable salt” refers to those salts whichare, within the scope of sound medical judgment, suitable for use incontact with the tissues of humans and lower animals without unduetoxicity, irritation, allergic response, and the like, and arecommensurate with a reasonable benefit/risk ratio. Pharmaceuticallyacceptable salts are well known in the art. For example, Berge et al.describe pharmaceutically acceptable salts in detail in J.Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein byreference. Pharmaceutically acceptable salts of the compounds describedherein include those derived from suitable inorganic and organic acidsand bases. Examples of pharmaceutically acceptable, nontoxic acidaddition salts are salts of an amino group formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuricacid, and perchloric acid or with organic acids such as acetic acid,oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, ormalonic acid or by using other methods known in the art such as ionexchange. Other pharmaceutically acceptable salts include adipate,alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate,borate, butyrate, camphorate, camphorsulfonate, citrate,cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate,formate, fumarate, glucoheptonate, glycerophosphate, gluconate,hemisulfate, heptanoate, hexanoate, hydroiodide,2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, laurylsulfate, malate, maleate, malonate, methanesulfonate,2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate,pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate,pivalate, propionate, stearate, succinate, sulfate, tartrate,thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and thelike. Salts derived from appropriate bases include alkali metal,alkaline earth metal, ammonium, and N⁺(C₁₋₄ alkyl)₄ ⁻ salts.Representative alkali or alkaline earth metal salts include sodium,lithium, potassium, calcium, magnesium, and the like. Furtherpharmaceutically acceptable salts include, when appropriate, nontoxicammonium, quaternary ammonium, and amine cations formed usingcounterions such as halide, hydroxide, carboxylate, sulfate, phosphate,nitrate, lower alkyl sulfonate, and aryl sulfonate.

The term “solvate” refers to forms of the compound, or a salt thereof,that are associated with a solvent, usually by a solvolysis reaction.This physical association may include hydrogen bonding. Conventionalsolvents include water, methanol, ethanol, acetic acid, DMSO, THF,diethyl ether, and the like. The compounds described herein may beprepared, e.g., in crystalline form, and may be solvated. Suitablesolvates include pharmaceutically acceptable solvates and furtherinclude both stoichiometric solvates and non-stoichiometric solvates. Incertain instances, the solvate will be capable of isolation, forexample, when one or more solvent molecules are incorporated in thecrystal lattice of a crystalline solid. “Solvate” encompasses bothsolution-phase and isolatable solvates. Representative solvates includehydrates, ethanolates, and methanolates.

The term “hydrate” refers to a compound that is associated with water.Typically, the number of the water molecules contained in a hydrate of acompound is in a definite ratio to the number of the compound moleculesin the hydrate. Therefore, a hydrate of a compound may be represented,for example, by the general formula R.xH₂O, wherein R is the compound,and x is a number greater than 0. A given compound may form more thanone type of hydrate, including, e.g., monohydrates (x is 1), lowerhydrates (x is a number greater than 0 and smaller than 1, e.g.,hemihydrates (R.0.5H₂O)), and polyhydrates (x is a number greater than1, e.g., dihydrates (R.2H₂O) and hexahydrates (R.6H₂O)).

The term “tautomers” or “tautomeric” refers to two or moreinterconvertable compounds resulting from at least one formal migrationof a hydrogen atom and at least one change in valency (e.g., a singlebond to a double bond, a triple bond to a single bond, or vice versa).The exact ratio of the tautomers depends on several factors, includingtemperature, solvent, and pH. Tautomerizations (i.e., the reactionproviding a tautomeric pair) may catalyzed by acid or base. Exemplarytautomerizations include keto-to-enol, amide-to-imide, lactam-to-lactim,enamine-to-imine, and enamine-to-(a different enamine) tautomerizations.

It is also to be understood that compounds that have the same molecularformula but differ in the nature or sequence of bonding of their atomsor the arrangement of their atoms in space are termed “isomers”. Isomersthat differ in the arrangement of their atoms in space are termed“stereoisomers”.

Stereoisomers that are not mirror images of one another are termed“diastereomers” and those that are non-superimposable mirror images ofeach other are termed “enantiomers”. When a compound has an asymmetriccenter, for example, it is bonded to four different groups, a pair ofenantiomers is possible. An enantiomer can be characterized by theabsolute configuration of its asymmetric center and is described by theR- and S-sequencing rules of Cahn and Prelog, or by the manner in whichthe molecule rotates the plane of polarized light and designated asdextrorotatory or levorotatory (i.e., as (+) or (−)-isomersrespectively). A chiral compound can exist as either individualenantiomer or as a mixture thereof. A mixture containing equalproportions of the enantiomers is called a “racemic mixture”.

The term “polymorphs” refers to a crystalline form of a compound (or asalt, hydrate, or solvate thereof) in a particular crystal packingarrangement. All polymorphs have the same elemental composition.Different crystalline forms usually have different X-ray diffractionpatterns, infrared spectra, melting points, density, hardness, crystalshape, optical and electrical properties, stability, and solubility.Recrystallization solvent, rate of crystallization, storage temperature,and other factors may cause one crystal form to dominate. Variouspolymorphs of a compound can be prepared by crystallization underdifferent conditions.

The term “prodrugs” refers to compounds, including derivatives of thecompounds described herein, which have cleavable groups and become bysolvolysis or under physiological conditions the compounds describedherein, which are pharmaceutically active in vivo. Such examplesinclude, but are not limited to, choline ester derivatives and the like,N-alkylmorpholine esters and the like. Other derivatives of thecompounds described herein have activity in both their acid and acidderivative forms, but in the acid sensitive form often offer advantagesof solubility, tissue compatibility, or delayed release in the mammalianorganism (see, Bundgard, H., Design of Prodrugs, pp. 7-9, 21-24,Elsevier, Amsterdam 1985). Prodrugs include acid derivatives well knownto practitioners of the art, such as, for example, esters prepared byreaction of the parent acid with a suitable alcohol, or amides preparedby reaction of the parent acid compound with a substituted orunsubstituted amine, or acid anhydrides, or mixed anhydrides. Simplealiphatic or aromatic esters, amides, and anhydrides derived from acidicgroups pendant on the compounds described herein are particularprodrugs. In some cases it is desirable to prepare double ester typeprodrugs such as (acyloxy)alkyl esters or((alkoxycarbonyl)oxy)alkylesters. C₁-C₈ alkyl, C₂-C₈ alkenyl, C₂-C₈alkynyl, aryl, C₇-C₁₂ substituted aryl, and C₇-C₁₂ arylalkyl esters ofthe compounds described herein may be preferred.

The term “small molecule” refers to molecules, whethernaturally-occurring or artificially created (e.g., via chemicalsynthesis) that have a relatively low molecular weight. Typically, asmall molecule is an organic compound (i.e., it contains carbon). Thesmall molecule may contain multiple carbon-carbon bonds, stereocenters,and other functional groups (e.g., amines, hydroxyl, carbonyls, andheterocyclic rings, etc.). In certain embodiments, the molecular weightof a small molecule is at most about 1,000 g/mol, at most about 900g/mol, at most about 800 g/mol, at most about 700 g/mol, at most about600 g/mol, at most about 500 g/mol, at most about 400 g/mol, at mostabout 300 g/mol, at most about 200 g/mol, or at most about 100 g/mol. Incertain embodiments, the molecular weight of a small molecule is atleast about 100 g/mol, at least about 200 g/mol, at least about 300g/mol, at least about 400 g/mol, at least about 500 g/mol, at leastabout 600 g/mol, at least about 700 g/mol, at least about 800 g/mol, orat least about 900 g/mol, or at least about 1,000 g/mol. Combinations ofthe above ranges (e.g., at least about 200 g/mol and at most about 500g/mol) are also possible. In certain embodiments, the small molecule isa therapeutically active agent such as a drug (e.g., a molecule approvedby the U.S. Food and Drug Administration as provided in the Code ofFederal Regulations (C.F.R.)). The small molecule may also be complexedwith one or more metal atoms and/or metal ions. In this instance, thesmall molecule is also referred to as a “small organometallic molecule.”Preferred small molecules are biologically active in that they produce abiological effect in animals, preferably mammals, more preferablyhumans. Small molecules include, but are not limited to, radionuclidesand imaging agents. In certain embodiments, the small molecule is adrug. Preferably, though not necessarily, the drug is one that hasalready been deemed safe and effective for use in humans or animals bythe appropriate governmental agency or regulatory body. For example,drugs approved for human use are listed by the FDA under 21 C.F.R.§§330.5, 331 through 361, and 440 through 460, incorporated herein byreference; drugs for veterinary use are listed by the FDA under 21C.F.R. §§500 through 589, incorporated herein by reference. All listeddrugs are considered acceptable for use in accordance with the presentinvention.

A “protein,” “peptide,” or “polypeptide” comprises a polymer of aminoacid residues linked together by peptide bonds and refers to proteins,polypeptides, and peptides of any size, structure, or function.Typically, a protein will be at least three amino acids long. A proteinmay refer to an individual protein or a collection of proteins. Proteinsdescribed herein preferably contain only natural amino acids, althoughnon-natural amino acids (i.e., compounds that do not occur in nature butthat can be incorporated into a polypeptide chain) and/or amino acidanalogs as are known in the art may alternatively be employed. Also, oneor more of the amino acids in a protein may be modified, for example, bythe addition of a chemical entity such as a carbohydrate group, ahydroxyl group, a phosphate group, a farnesyl group, an isofarnesylgroup, a fatty acid group, a linker for conjugation orfunctionalization, or other modification. A protein may also be a singlemolecule or may be a multi-molecular complex. A protein may be afragment of a naturally occurring protein or peptide. A protein may benaturally occurring, recombinant, synthetic, or any combination ofthese.

The term “gene” refers to a nucleic acid fragment that expresses aspecific protein, including regulatory sequences preceding (5′non-coding sequences) and following (3′ non-coding sequences) the codingsequence. “Native gene” refers to a gene as found in nature with its ownregulatory sequences. “Chimeric gene” or “chimeric construct” refers toany gene or a construct, not a native gene, comprising regulatory andcoding sequences that are not found together in nature. Accordingly, achimeric gene or chimeric construct may comprise regulatory sequencesand coding sequences that are derived from different sources, orregulatory sequences and coding sequences derived from the same source,but arranged in a manner different than that found in nature.“Endogenous gene” refers to a native gene in its natural location in thegenome of an organism. A “foreign” gene refers to a gene not normallyfound in the host organism, but which is introduced into the hostorganism by gene transfer. Foreign genes can comprise native genesinserted into a non-native organism, or chimeric genes. A “transgene” isa gene that has been introduced into the genome by a transformationprocedure.

The term “histone” refers to highly alkaline proteins found ineukaryotic cell nuclei that package and order the DNA into structuralunits called nucleosomes. They are the chief protein components ofchromatin, acting as spools around which DNA winds, and play a role ingene regulation. In certain embodiments, the histone is histone H1(e.g., histone H1F, histone H1H1). In certain embodiments, the histoneis histone H2A (e.g., histone H2AF, histone H2A1, histone H2A2). Incertain embodiments, the histone is histone H2B (e.g., histone H2BF,histone H2B1, histone H2B2). In certain embodiments, the histone ishistone H3 (e.g., histone H3A1, histone H3A2, histone H3A3). In certainembodiments, the histone is histone H4 (e.g., histone H41, histone H44).

The term “bromodomain” refers to a protein domain that recognizesacetylated lysine residues such as those on the N-terminal tails ofhistones. In certain embodiments, a bromodomain of a BET proteincomprises about 110 amino acids and shares a conserved fold comprising aleft-handed bundle of four alpha helices linked by diverse loop regionsthat interact with chromatin. In certain embodiments, the bromodomain isASH1L (GenBank ID: gi|8922081), ATAD2 (GenBank ID: gi|24497618), BAZ2B(GenBank ID: gi|7304923), BRD1 (GenBank ID: gi|11321642), BRD2(1)(GenBank ID: gi|4826806), BRD2(2) (GenBank ID: gi|4826806), BRD3(1)(GenBank ID: gi|11067749), BRD3(2) (GenBank ID: gi|11067749), BRD4(1)(GenBank ID: gi|19718731), BRD4(2) (GenBank ID: gi|19718731), BRD9(GenBank ID: gi|57770383), BRDT(1) (GenBank ID: gi|46399198), BRPF1(GenBank ID: gi|51173720), CECR2 (GenBank ID: gi|148612882), CREBBP(GenBank ID: gi|4758056), EP300 (GenBank ID: gi|50345997), FALZ (GenBankID: gi|38788274), GCN5L2 (GenBank ID: gi|10835101), KIAA1240 (GenBankID: gi|51460532), LOC93349 (GenBank ID: gi|134133279), PB1(1) (GenBankID: gi|30794372), PB1(2) (GenBank ID: gi|30794372), PB1(3) (GenBank ID:gi|30794372), PB1(5) (GenBank ID: gi|30794372), PB1(6) (GenBank ID:gi|30794372), PCAF (GenBank ID: gi|140805843), PHIP(2) (GenBank ID:gi|34996489), SMARCA2 (GenBank ID: gi|48255900), SMARCA4 (GenBank ID:gi|21071056), SP140 (GenBank ID: gi|52487219), TAF1(1) (GenBank ID:gi|20357585), TAF1(2) (GenBank ID: gi|20357585), TAF1L(1) (GenBank ID:gi|24429572), TAF1L(2) (GenBank ID: gi|24429572), TIF1 (GenBank ID:gi|14971415), TRIM28 (GenBank ID: gi|5032179), or WDR9(2) (GenBank ID:gi|116445436).

The term “bromodomain-containing protein” or “bromodomain protein”refers to a protein, whether wild-type or mutant, natural or synthetic,truncated or complete, or a variant thereof, that possesses the minimumamino acid sequence sufficient for a functional bromodomain capable ofmediating molecular recognition of acetyl-lysine of acetylated lysineresidues on a second protein (e.g., a histone), such as on the tails ofhistones. Bromodomain-containing proteins include, for example, fusionproteins comprising a bromodomain and an additional portion havingdesired functionality (e.g., a reporter portion). Exemplary bromodomainsinclude, but are not limited to, bromodomains in

The terms “composition” and “formulation” are used interchangeably.

A “subject” to which administration is contemplated includes, but is notlimited to, humans (i.e., a male or female of any age group, e.g., apediatric subject (e.g., infant, child, adolescent) or adult subject(e.g., young adult, middle-aged adult, or senior adult)) and/or othernon-human animals, for example, mammals (e.g., primates (e.g.,cynomolgus monkeys, rhesus monkeys); commercially relevant mammals suchas cattle, pigs, horses, sheep, goats, cats, and/or dogs) and birds(e.g., commercially relevant birds such as chickens, ducks, geese,and/or turkeys). In certain embodiments, the animal is a mammal. Theanimal may be a male or female at any stage of development. The animalmay be a transgenic animal or genetically engineered animal. In certainembodiments, the subject is non-human animal. In certain embodiments,the animal is fish. A “patient” refers to a human subject in need oftreatment of a disease. The subject may also be a plant. In certainembodiments, the plant is a land plant. In certain embodiments, theplant is a non-vascular land plant. In certain embodiments, the plant isa vascular land plant. In certain embodiments, the plant is a seedplant. In certain embodiments, the plant is a cultivated plant. Incertain embodiments, the plant is a dicot. In certain embodiments, theplant is a monocot. In certain embodiments, the plant is a floweringplant. In some embodiments, the plant is a cereal plant, e.g., maize,corn, wheat, rice, oat, barley, rye, or millet. In some embodiments, theplant is a legume, e.g., a bean plant, e.g., soybean plant. In someembodiments, the plant is a tree or shrub.

The terms “administer,” “administering,” or “administration” refers toimplanting, absorbing, ingesting, injecting, inhaling, or otherwiseintroducing a compound described herein, or a composition thereof, in oron a subject.

The terms “treatment,” “treat,” and “treating” refer to reversing,alleviating, delaying the onset of, or inhibiting the progress of adisease described herein. In some embodiments, treatment may beadministered after one or more signs or symptoms of the disease havedeveloped or have been observed. In other embodiments, treatment may beadministered in the absence of signs or symptoms of the disease. Forexample, treatment may be administered to a susceptible subject prior tothe onset of symptoms (e.g., in light of a history of symptoms and/or inlight of exposure to a pathogen). Treatment may also be continued aftersymptoms have resolved, for example, to delay or prevent recurrence.

The terms “condition,” “disease,” and “disorder” are usedinterchangeably.

An “effective amount” of a compound described herein refers to an amountsufficient to elicit the desired biological response, i.e., treating thecondition. As will be appreciated by those of ordinary skill in thisart, the effective amount of a compound described herein may varydepending on such factors as the desired biological endpoint, thepharmacokinetics of the compound, the condition being treated, the modeof administration, and the age and health of the subject. An effectiveamount encompasses therapeutic and prophylactic treatment.

A “therapeutically effective amount” of a compound described herein isan amount sufficient to provide a therapeutic benefit in the treatmentof a condition or to delay or minimize one or more symptoms associatedwith the condition. A therapeutically effective amount of a compoundmeans an amount of therapeutic agent, alone or in combination with othertherapies, which provides a therapeutic benefit in the treatment of thecondition. The term “therapeutically effective amount” can encompass anamount that improves overall therapy, reduces or avoids symptoms, signs,or causes of the condition, and/or enhances the therapeutic efficacy ofanother therapeutic agent. In certain embodiments, a therapeuticallyeffective amount is effective for inhibiting the activity of abromodomain-containing protein. In certain embodiments, atherapeutically effective amount is effective for treating a diseasedescribed herein. In certain embodiments, a therapeutically effectiveamount is effective for inhibiting the activity of abromodomain-containing protein and for treating a disease describedherein.

A “prophylactically effective amount” of a compound described herein isan amount sufficient to prevent a condition, or one or more symptomsassociated with the condition or prevent its recurrence. Aprophylactically effective amount of a compound means an amount of atherapeutic agent, alone or in combination with other agents, whichprovides a prophylactic benefit in the prevention of the condition. Theterm “prophylactically effective amount” can encompass an amount thatimproves overall prophylaxis or enhances the prophylactic efficacy ofanother prophylactic agent. In certain embodiments, a prophylacticallyeffective amount is effective for inhibiting the activity of abromodomain-containing protein. In certain embodiments, aprophylactically effective amount is effective for preventing a diseasedescribed herein. In certain embodiments, a prophylactically effectiveamount is effective for inhibiting the activity of abromodomain-containing protein and for preventing a disease describedherein.

A “proliferative disease” refers to a disease that occurs due toabnormal growth or extension by the multiplication of cells (Walker,Cambridge Dictionary of Biology; Cambridge University Press: Cambridge,UK, 1990). A proliferative disease may be associated with: 1) thepathological proliferation of normally quiescent cells; 2) thepathological migration of cells from their normal location (e.g.,metastasis of neoplastic cells); 3) the pathological expression ofproteolytic enzymes such as the matrix metalloproteinases (e.g.,collagenases, gelatinases, and elastases); or 4) the pathologicalangiogenesis as in proliferative retinopathy and tumor metastasis.Exemplary proliferative diseases include cancers (i.e., “malignantneoplasms”), benign neoplasms, angiogenesis, inflammatory diseases, andautoimmune diseases.

The term “angiogenesis” refers to the physiological process throughwhich new blood vessels form from pre-existing vessels. Angiogenesis isdistinct from vasculogenesis, which is the de novo formation ofendothelial cells from mesoderm cell precursors. The first vessels in adeveloping embryo form through vasculogenesis, after which angiogenesisis responsible for most blood vessel growth during normal or abnormaldevelopment. Angiogenesis is a vital process in growth and development,as well as in wound healing and in the formation of granulation tissue.However, angiogenesis is also a fundamental step in the transition oftumors from a benign state to a malignant one, leading to the use ofangiogenesis inhibitors in the treatment of cancer. Angiogenesis may bechemically stimulated by angiogenic proteins, such as growth factors(e.g., VEGF). “Pathological angiogenesis” refers to abnormal (e.g.,excessive or insufficient) angiogenesis that amounts to and/or isassociated with a disease.

The terms “neoplasm” and “tumor” are used interchangeably and refer toan abnormal mass of tissue wherein the growth of the mass surpasses andis not coordinated with the growth of a normal tissue. A neoplasm ortumor may be “benign” or “malignant,” depending on the followingcharacteristics: degree of cellular differentiation (includingmorphology and functionality), rate of growth, local invasion, andmetastasis. A “benign neoplasm” is generally well differentiated, hascharacteristically slower growth than a malignant neoplasm, and remainslocalized to the site of origin. In addition, a benign neoplasm does nothave the capacity to infiltrate, invade, or metastasize to distantsites. Exemplary benign neoplasms include, but are not limited to,lipoma, chondroma, adenomas, acrochordon, senile angiomas, seborrheickeratoses, lentigos, and sebaceous hyperplasias. In some cases, certain“benign” tumors may later give rise to malignant neoplasms, which mayresult from additional genetic changes in a subpopulation of the tumor'sneoplastic cells, and these tumors are referred to as “pre-malignantneoplasms.” An exemplary pre-malignant neoplasm is a teratoma. Incontrast, a “malignant neoplasm” is generally poorly differentiated(anaplasia) and has characteristically rapid growth accompanied byprogressive infiltration, invasion, and destruction of the surroundingtissue. Furthermore, a malignant neoplasm generally has the capacity tometastasize to distant sites. The term “metastasis,” “metastatic,” or“metastasize” refers to the spread or migration of cancerous cells froma primary or original tumor to another organ or tissue and is typicallyidentifiable by the presence of a “secondary tumor” or “secondary cellmass” of the tissue type of the primary or original tumor and not ofthat of the organ or tissue in which the secondary (metastatic) tumor islocated. For example, a prostate cancer that has migrated to bone issaid to be metastasized prostate cancer and includes cancerous prostatecancer cells growing in bone tissue.

The term “cancer” refers to a malignant neoplasm (Stedman's MedicalDictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia,1990). Exemplary cancers include, but are not limited to, acousticneuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma(e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma);appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g.,cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinomaof the breast, papillary carcinoma of the breast, mammary cancer,medullary carcinoma of the breast); brain cancer (e.g., meningioma,glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma),medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer(e.g., cervical adenocarcinoma); choriocarcinoma; chordoma;craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer,colorectal adenocarcinoma); connective tissue cancer; epithelialcarcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma,multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g.,uterine cancer, uterine sarcoma); esophageal cancer (e.g.,adenocarcinoma of the esophagus, Barrett's adenocarcinoma); Ewing'ssarcoma; ocular cancer (e.g., intraocular melanoma, retinoblastoma);familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g.,stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germcell cancer; head and neck cancer (e.g., head and neck squamous cellcarcinoma, oral cancer (e.g., oral squamous cell carcinoma), throatcancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngealcancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemiasuch as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL),acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronicmyelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chroniclymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphomasuch as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) andnon-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large celllymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicularlymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma(CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas(e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodalmarginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma),primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacyticlymphoma (i.e., Waldenström's macroglobulinemia), hairy cell leukemia(HCL), immunoblastic large cell lymphoma, precursor B-lymphoblasticlymphoma and primary central nervous system (CNS) lymphoma; and T-cellNHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheralT-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g.,mycosis fungoides, Sezary syndrome), angioimmunoblastic T-cell lymphoma,extranodal natural killer T-cell lymphoma, enteropathy type T-celllymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplasticlarge cell lymphoma); a mixture of one or more leukemia/lymphoma asdescribed above; and multiple myeloma (MM)), heavy chain disease (e.g.,alpha chain disease, gamma chain disease, mu chain disease);hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastictumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastomaa.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g.,hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g.,bronchogenic carcinoma, small cell lung cancer (SCLC), non-small celllung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS);mastocytosis (e.g., systemic mastocytosis); muscle cancer;myelodysplastic syndrome (MDS); mesothelioma; myeloproliferativedisorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis(ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF),chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML),chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES));neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreaticneuroendocrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g.,bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarianembryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma;pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductalpapillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer(e.g., Paget's disease of the penis and scrotum); pinealoma; primitiveneuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplasticsyndromes; intraepithelial neoplasms; prostate cancer (e.g., prostateadenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer;skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA),melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g.,appendix cancer); soft tissue sarcoma (e.g., malignant fibroushistiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor(MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous glandcarcinoma; small intestine cancer; sweat gland carcinoma; synovioma;testicular cancer (e.g., seminoma, testicular embryonal carcinoma);thyroid cancer (e.g., papillary carcinoma of the thyroid, papillarythyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer;vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).

The term “inflammatory disease” refers to a disease caused by, resultingfrom, or resulting in inflammation. The term “inflammatory disease” mayalso refer to a dysregulated inflammatory reaction that causes anexaggerated response by macrophages, granulocytes, and/or T-lymphocytesleading to abnormal tissue damage and/or cell death. An inflammatorydisease can be either an acute or chronic inflammatory condition and canresult from infections or non-infectious causes. Inflammatory diseasesinclude, without limitation, atherosclerosis, arteriosclerosis,autoimmune disorders, multiple sclerosis, systemic lupus erythematosus,polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis,tendonitis, bursitis, psoriasis, cystic fibrosis, arthrosteitis,rheumatoid arthritis, inflammatory arthritis, Sjogren's syndrome, giantcell arteritis, progressive systemic sclerosis (scleroderma), ankylosingspondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid,diabetes (e.g., Type I), myasthenia gravis, Hashimoto's thyroiditis,Graves' disease, Goodpasture's disease, mixed connective tissue disease,sclerosing cholangitis, inflammatory bowel disease, Crohn's disease,ulcerative colitis, pernicious anemia, inflammatory dermatoses, usualinterstitial pneumonitis (UIP), asbestosis, silicosis, bronchiectasis,berylliosis, talcosis, pneumoconiosis, sarcoidosis, desquamativeinterstitial pneumonia, lymphoid interstitial pneumonia, giant cellinterstitial pneumonia, cellular interstitial pneumonia, extrinsicallergic alveolitis, Wegener's granulomatosis and related forms ofangiitis (temporal arteritis and polyarteritis nodosa), inflammatorydermatoses, delayed-type hypersensitivity reactions (e.g., poison ivydermatitis), pneumonia, respiratory tract inflammation, AdultRespiratory Distress Syndrome (ARDS), encephalitis, immediatehypersensitivity reactions, asthma, hayfever, allergies, acuteanaphylaxis, rheumatic fever, glomerulonephritis, pyelonephritis,cellulitis, cystitis, chronic cholecystitis, ischemia (ischemic injury),reperfusion injury, allograft rejection, host-versus-graft rejection,appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis,cervicitis, cholangitis, chorioamnionitis, conjunctivitis,dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis,enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis,gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis,myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis,osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis,pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis,salpingitis, sinusitis, stomatitis, synovitis, testitis, tonsillitis,urethritis, urocystitis, uveitis, vaginitis, vasculitis, vulvitis,vulvovaginitis, angitis, chronic bronchitis, osteomyelitis, opticneuritis, temporal arteritis, transverse myelitis, necrotizingfasciitis, and necrotizing enterocolitis. An ocular inflammatory diseaseincludes, but is not limited to, post-surgical inflammation.

An “autoimmune disease” refers to a disease arising from aninappropriate immune response of the body of a subject againstsubstances and tissues normally present in the body. In other words, theimmune system mistakes some part of the body as a pathogen and attacksits own cells. This may be restricted to certain organs (e.g., inautoimmune thyroiditis) or involve a particular tissue in differentplaces (e.g., Goodpasture's disease which may affect the basementmembrane in both the lung and kidney). The treatment of autoimmunediseases is typically with immunosuppression, e.g., medications whichdecrease the immune response. Exemplary autoimmune diseases include, butare not limited to, glomerulonephritis, Goodpasture's syndrome,necrotizing vasculitis, lymphadenitis, peri-arteritis nodosa, systemiclupus erythematosis, rheumatoid, arthritis, psoriatic arthritis,systemic lupus erythematosis, psoriasis, ulcerative colitis, systemicsclerosis, dermatomyositis/polymyositis, anti-phospholipid antibodysyndrome, scleroderma, pemphigus vulgaris, ANCA-associated vasculitis(e.g., Wegener's granulomatosis, microscopic polyangiitis), uveitis,Sjogren's syndrome, Crohn's disease, Reiter's syndrome, ankylosingspondylitis, Lyme disease, Guillain-Barré syndrome, Hashimoto'sthyroiditis, and cardiomyopathy.

A “kinase” is a type of enzyme that transfers phosphate groups from highenergy donor molecules, such as ATP, to specific substrates, referred toas phosphorylation. Kinases are part of the larger family ofphosphotransferases. One of the largest groups of kinases are proteinkinases, which act on and modify the activity of specific proteins.Kinases are used extensively to transmit signals and control complexprocesses in cells. Various other kinases act on small molecules such aslipids, carbohydrates, amino acids, and nucleotides, either forsignaling or to prime them for metabolic pathways. Kinases are oftennamed after their substrates. More than 500 different protein kinaseshave been identified in humans. These exemplary human protein kinasesinclude, but are not limited to, AAK1, ABL, ACK, ACTR2, ACTR2B, AKT1,AKT2, AKT3, ALK, ALK1, ALK2, ALK4, ALK7, AMPKa1, AMPKa2, ANKRD3, ANPa,ANPb, ARAF, ARAFps, ARG, AurA, AurAps1, AurAps2, AurB, AurBps1, AurC,AXL, BARK1, BARK2, BIKE, BLK, BMPR1A, BMPR1Aps1, BMPR1Aps2, BMPR1B,BMPR2, BMX, BRAF, BRAFps, BRK, BRSK1, BRSK2, BTK, BUB1, BUBR1, CaMK1a,CaMK1b, CaMK1d, CaMK1g, CaMK2a, CaMK2b, CaMK2d, CaMK2g, CaMK4, CaMKK1,CaMKK2, caMLCK, CASK, CCK4, CCRK, CDC2, CDC7, CDK10, CDK11, CDK2, CDK3,CDK4, CDK4ps, CDK5, CDK5ps, CDK6, CDK7, CDK7ps, CDK8, CDK8ps, CDK9,CDKL1, CDKL2, CDKL3, CDKL4, CDKL5, CGDps, CHED, CHK1, CHK2, CHK2ps1,CHK2ps2, CK1a, CK1a2, CK1aps1, CK1aps2, CK1aps3, CK1d, CK1e, CK1g1,CK1g2, CK1g2ps, CK1g3, CK2a1, CK2a1-rs, CK2a2, CLIK1, CLIK1L, CLK1,CLK2, CLK2ps, CLK3, CLK3ps, CLK4, COT, CRIK, CRK7, CSK, CTK, CYGD, CYGF,DAPK1, DAPK2, DAPK3, DCAMKL1, DCAMKL2, DCAMKL3, DDR1, DDR2, DLK, DMPK1,DMPK2, DRAK1, DRAK2, DYRK1A, DYRK1B, DYRK2, DYRK3, DYRK4, EGFR, EphA1,EphA10, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphB1, EphB2,EphB3, EphB4, EphB6, Erk1, Erk2, Erk3, Erk3ps1, Erk3ps2, Erk3ps3,Erk3ps4, Erk4, Erk5, Erk7, FAK, FER, FERps, FES, FGFR1, FGFR2, FGFR3,FGFR4, FGR, FLT1, FLT1ps, FLT3, FLT4, FMS, FRK, Fused, FYN, GAK, GCK,GCN2, GCN22, GPRK4, GPRK5, GPRK6, GPRK6ps, GPRK7, GSK3A, GSK3B, Haspin,HCK, HER2/ErbB2, HER3/ErbB3, HER4/ErbB4, HH498, HIPK1, HIPK2, HIPK3,HIPK4, HPK1, HRI, HRIps, HSER, HUNK, ICK, IGF1R, IKKa, IKKb, IKKe, ILK,INSR, IRAK1, IRAK2, IRAK3, IRAK4, IRE1, IRE2, IRR, ITK, JAK1, JAK12,JAK2, JAK22, JAK3, JAK32, JNK1, JNK2, JNK3, KDR, KHS1, KHS2, KIS, KIT,KSGCps, KSR1, KSR2, LATS1, LATS2, LCK, LIMK1, LIMK2, LIMK2ps, LKB1,LMR1, LMR2, LMR3, LOK, LRRK1, LRRK2, LTK, LYN, LZK, MAK, MAP2K1,MAP2K1ps, MAP2K2, MAP2K2ps, MAP2K3, MAP2K4, MAP2K5, MAP2K6, MAP2K7,MAP3K1, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP3K6, MAP3K7, MAP3K8,MAPKAPK2, MAPKAPK3, MAPKAPK5, MAPKAPKps1, MARK1, MARK2, MARK3, MARK4,MARKps01, MARKps02, MARKps03, MARKps04, MARKps05, MARKps07, MARKps08,MARKps09, MARKps10, MARKps11, MARKps12, MARKps13, MARKps15, MARKps16,MARKps17, MARKps18, MARKps19, MARKps20, MARKps21, MARKps22, MARKps23,MARKps24, MARKps25, MARKps26, MARKps27, MARKps28, MARKps29, MARKps30,MAST1, MAST2, MAST3, MAST4, MASTL, MELK, MER, MET, MISR2, MLK1, MLK2,MLK3, MLK4, MLKL, MNK1, MNK1ps, MNK2, MOK, MOS, MPSK1, MPSK1ps, MRCKa,MRCKb, MRCKps, MSK1, MSK12, MSK2, MSK22, MSSK1, MST1, MST2, MST3,MST3ps, MST4, MUSK, MYO3A, MYO3B, MYT1, NDR1, NDR2, NEK1, NEK10, NEK11,NEK2, NEK2ps1, NEK2ps2, NEK2ps3, NEK3, NEK4, NEK4ps, NEK5, NEK6, NEK7,NEK8, NEK9, NIK, NIM1, NLK, NRBP1, NRBP2, NuaK1, NuaK2, Obscn, Obscn2,OSR1, p38a, p38b, p38d, p38g, p70S6K, p70S6Kb, p70S6Kps1, p70S6Kps2,PAK1, PAK2, PAK2ps, PAK3, PAK4, PAK5, PAK6, PASK, PBK, PCTAIRE1,PCTAIRE2, PCTAIRE3, PDGFRa, PDGFRb, PDK1, PEK, PFTAIRE1, PFTAIRE2,PHKg1, PHKg1ps1, PHKg1ps2, PHKg1ps3, PHKg2, PIK3R4, PIM1, PIM2, PIM3,PINK1, PITSLRE, PKACa, PKACb, PKACg, PKCa, PKCb, PKCd, PKCe, PKCg, PKCh,PKCi, PKCips, PKCt, PKCz, PKD1, PKD2, PKD3, PKG1, PKG2, PKN1, PKN2,PKN3, PKR, PLK1, PLK1ps1, PLK1ps2, PLK2, PLK3, PLK4, PRKX, PRKXps, PRKY,PRP4, PRP4ps, PRPK, PSKH1, PSKH1ps, PSKH2, PYK2, QIK, QSK, RAF1, RAF1ps,RET, RHOK, RIPK1, RIPK2, RIPK3, RNAseL, ROCK1, ROCK2, RON, ROR1, ROR2,ROS, RSK1, RSK12, RSK2, RSK22, RSK3, RSK32, RSK4, RSK42, RSKL1, RSKL2,RYK, RYKps, SAKps, SBK, SCYL1, SCYL2, SCYL2ps, SCYL3, SGK, SgK050ps,SgK069, SgK071, SgK085, SgK110, SgK196, SGK2, SgK223, SgK269, SgK288,SGK3, SgK307, SgK384ps, SgK396, SgK424, SgK493, SgK494, SgK495, SgK496,SIK, skMLCK, SLK, Slob, smMLCK, SNRK, SPEG, SPEG2, SRC, SRM, SRPK1,SRPK2, SRPK2ps, SSTK, STK33, STK33ps, STLK3, STLK5, STLK6, STLK6ps1,STLK6-rs, SuRTK106, SYK, TAK1, TAO1, TAO2, TAO3, TBCK, TBK1, TEC, TESK1,TESK2, TGFbR1, TGFbR2, TIE1, TIE2, TLK1, TLK1ps, TLK2, TLK2ps1, TLK2ps2,TNK1, Trad, Trb1, Trb2, Trb3, Trio, TRKA, TRKB, TRKC, TSSK1, TSSK2,TSSK3, TSSK4, TSSKps1, TSSKps2, TTBK1, TTBK2, TTK, TTN, TXK, TYK2,TYK22, TYRO3, TYRO3ps, ULK1, ULK2, ULK3, ULK4, VACAMKL, VRK1, VRK2,VRK3, VRK3ps, Wee1, Wee1B, Wee1Bps, Wee1ps1, Wee1ps2, Wnk1, Wnk2, Wnk3,Wnk4, YANK1, YANK2, YANK3, YES, YESps, YSK1, ZAK, ZAP70, ZC1/HGK,ZC2/TNIK, ZC3/MINK, ZC4/NRK.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the results of an exemplary measurement of K_(d) values ofan exemplary compound as measured by Isothermal Titration Calorimetery(ITC) at BRD4.1.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

Recently, some compounds have been reported to be bromodomain bindingagents, e.g., WO 2012/075383, WO 2011/054553, WO 2011/054841, WO2011/054844, WO 2011/054845, WO 2011/054846, WO 2011/054848, WO2011/143669, and WO 2011/161031. Moreover, Japanese patent applicationpublication JP 2008/156311 discloses a benzimidazole derivative which issaid to be a BRD2 bromodomain binding agent which has utility withrespect to virus infection and/or proliferation. International PCTpublication WO 2009/084693 discloses a series of thienotriazolodiazepinederivatives that are said to inhibit the binding between an acetylatedhistone and a bromodomain-containing protein which are said to be usefulas anti-cancer agents. International PCT publication WO 2011/054843suggests compounds which inhibit the binding of a bromodomain with itscognate acetylated proteins may have utility in the treatment of a rangeof autoimmune and inflammatory diseases or conditions. However, thereremains a need for additional potent and safe bromodomain binders.

The present invention provides compounds of Formula (II) (e.g.,compounds of Formula (I)), which are binders of bromodomains and/orbromodomain-containing proteins. The compounds described herein may beable to bind to in a binding pocket of a bromodomain (e.g., abromodomain of a bromodomain-containing protein). Without wishing to bebound by any particular theory, the compounds described herein may bindto the binding pocket of a bromodomain by mimicking the contact betweenan acetylated lysine residue of a second protein (e.g., a histone) andthe binding pocket. In certain embodiments, the compounds describedherein bind to the binding pocket of the bromodomain. The compounddescribed herein may also be inhibitors of bromodomains and/orbromodomain-containing proteins. Also provided in the present inventionare pharmaceutical compositions, methods, uses, and kits useful ininhibiting the activity of a bromodomain-containing protein (e.g., atranscription factor). The compounds, pharmaceutical compositions,methods, uses, and kits may be useful in treating and/or preventingdiseases associated with a bromodomain, diseases associated with abromodomain-containing protein, diseases associated with the activity(e.g., aberrant activity) of a bromodomain, and diseases associated withthe activity (e.g., aberrant activity) of a bromodomain-containingprotein. Exemplary diseases that maybe prevented and/or treated withcompounds described herein include proliferative diseases (e.g.,cancers, benign neoplasms, angiogenesis, inflammatory diseases, andautoimmune diseases), autoimmune diseases, cardiovascular diseases,viral infections, fibrotic diseases, metabolic diseases, endocrinediseases, and radiation poisoning. The compounds, pharmaceuticalcompositions, methods, uses, and kits may also be useful for malecontraception and for inhibiting the replication of or killing a virus.

Compounds

In one aspect, the present invention provides compounds of Formula (II):

and pharmaceutically acceptable salts, solvates, hydrates, polymorphs,co-crystals, tautomers, stereoisomers, isotopically labeled derivatives,and prodrugs thereof, wherein:

is a single or double bond;

W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂, —S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂,—S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R_(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring;

each instance of R^(Z1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, an oxygen protecting group when attached to an oxygen atom,a sulfur protecting group when attached to a sulfur atom, or a nitrogenprotecting group when attached to a nitrogen atom, or two instances ofR^(Z1) are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring;

each instance of R^(A) is independently hydrogen, halogen, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, —OR^(A1),—N(R^(A1))₂, —SR^(A1), —CN, —SCN, —C(═NR^(A1))R^(A1),—C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂, —C(═O)R^(A1),—C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂, —NR^(A1)C(═O)R^(A1),—NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂, —OC(═O)R^(A1),—OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein each instance of R^(A1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, or a sulfur protecting group whenattached to a sulfur atom, or two R^(A1) groups are joined to form asubstituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring;

n is 0, 1, 2, 3, 4, 5, 6, 7, or 8;

X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance of R^(X) isindependently hydrogen, halogen, or substituted or unsubstituted C₁₋₆alkyl;

each instance of R^(B) is independently hydrogen, halogen, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, —OR^(B1),—N(R^(B1))₂, —SR^(B1), —CN, —SCN, —C(═NR^(B1))R^(B1),—C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂, —C(═O)R^(B1),—C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂, —NR^(B1)C(═O)R^(B1),—NR^(B1)C(═O)OR^(B1), —NR^(B1)C(═O)N(R^(B1))₂, —OC(═O)R^(B1),—OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein each instance of R^(B1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, or a sulfur protecting group whenattached to a sulfur atom, or two R^(B1) groups are joined to form asubstituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring;

m is 0, 1, 2, 3, or 4;

R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl;

R^(D) is hydrogen or substituted or unsubstituted alkyl;

R^(E) is hydrogen or substituted or unsubstituted alkyl;

R^(F) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl;

R^(G) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; and

R^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl;

or R^(G) and R^(H) are joined to form a substituted or unsubstitutedphenyl ring.

Formula (II) includes moiety W on the phenyl ring. In certainembodiments, W is —C(═O)OR^(Z1), optionally wherein R^(Z1) issubstituted or unsubstituted C₁₋₆ alkyl (e.g., Me), substituted orunsubstituted phenyl, or an oxygen protecting group. In certainembodiments, W is —C(═O)OH. In certain embodiments, W is —C(═O)OR^(Z1),wherein R^(Z1) is not H. In certain embodiments, W is —C(═O)N(R^(Z1))₂,optionally wherein each instance of R^(Z1) is independently substitutedor unsubstituted C₁₋₆ alkyl (e.g., Me), substituted or unsubstitutedphenyl, or a nitrogen protecting group, or optionally wherein twoinstances of R^(Z1) are joined to form a substituted or unsubstitutedheterocyclic ring or substituted or unsubstituted heteroaryl ring. Incertain embodiments, W is —C(═O)NHR^(Z1), optionally R^(Z1) issubstituted or unsubstituted C₁₋₆ alkyl (e.g., Me), substituted orunsubstituted phenyl, or a nitrogen protecting group. In certainembodiments, W is —C(═O)NH₂. In certain embodiments, W is —S(═O)OR^(Z1)or —S(═O)N(R^(Z1))₂, optionally wherein each instance of R^(Z1) isindependently substituted or unsubstituted C₁₋₆ alkyl (e.g., Me),substituted or unsubstituted phenyl, an oxygen protecting group whenattached to an oxygen atom, or a nitrogen protecting group when attachedto a nitrogen atom, or optionally wherein two instances of R^(Z1) arejoined to form a substituted or unsubstituted heterocyclic ring orsubstituted or unsubstituted heteroaryl ring. In certain embodiments, Wis —S(═O)OH. In certain embodiments, W is —S(═O)NH(R^(Z1)), optionallywherein R^(Z1) is substituted or unsubstituted C₁₋₆ alkyl (e.g., Me),substituted or unsubstituted phenyl, or a nitrogen protecting group. Incertain embodiments, W is —S(═O)NH₂. In certain embodiments, W is—S(═O)₂OR^(Z1), optionally wherein R^(Z1) is substituted orunsubstituted C₁₋₆ alkyl (e.g., Me), substituted or unsubstitutedphenyl, or an oxygen protecting group. In certain embodiments, W is—S(═O)₂OH. In certain embodiments, W is —S(═O)₂N(R^(Z1))₂, optionallywherein each instance of R^(Z1) is independently substituted orunsubstituted C₁₋₆ alkyl (e.g., Me), substituted or unsubstitutedphenyl, or a nitrogen protecting group, or optionally wherein twoinstances of R^(Z1) are joined to form a substituted or unsubstitutedheterocyclic ring or substituted or unsubstituted heteroaryl ring. Incertain embodiments, W is —S(═O)₂NH(R^(Z1)), optionally wherein R^(Z1)is substituted or unsubstituted C₁₋₆ alkyl (e.g., Me), substituted orunsubstituted phenyl, or a nitrogen protecting group. In certainembodiments, W is —S(═O)₂NH₂.

In certain embodiments, W is of the formula:

and thus a compound of Formula (II) is of Formula (I):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

Formula (I) or (II) includes a bond

. In certain embodiments,

is a single bond. In certain embodiments,

is a double bond.

Formula (I) includes a divalent moiety Z. In certain embodiments, Z is—O—. In certain embodiments, Z is —N(R^(Z))—. In certain embodiments, Zis —NH—. In certain embodiments, Z is —N(substituted or unsubstituted,C₁₋₆ alkyl)-. In certain embodiments, Z is —N(substituted orunsubstituted, 4- to 7-membered, monocyclic heterocyclyl)-. In certainembodiments, Z is —C(R^(Z))₂—. In certain embodiments, Z is —CH(R^(Z))—.In certain embodiments, Z is —CH(substituted or unsubstituted, C₁₋₆alkyl)-. In certain embodiments, Z is —CH(substituted or unsubstituted,4- to 7-membered, monocyclic heterocyclyl)-.

Formula (I) or (II) may include one or more substituents R^(Z) on thedivalent moiety Z. In certain embodiments, at least one instance ofR^(Z) is H. In certain embodiments, at least one instance of R^(Z) issubstituted acyl. In certain embodiments, at least one instance of R^(Z)is unsubstituted acyl. In certain embodiments, at least one instance ofR^(Z) is acetyl. In certain embodiments, at least one instance of R^(Z)is substituted alkyl. In certain embodiments, at least one instance ofR^(Z) is unsubstituted alkyl. In certain embodiments, at least oneinstance of R^(Z) is unsubstituted C₁₋₆ alkyl. In certain embodiments,at least one instance of R^(Z) is methyl. In certain embodiments, atleast one instance of R^(Z) is ethyl. In certain embodiments, at leastone instance of R^(Z) is propyl. In certain embodiments, at least oneinstance of R^(Z) is butyl. In certain embodiments, at least oneinstance of R^(Z) is pentyl. In certain embodiments, at least oneinstance of R^(Z) is hexyl. In certain embodiments, at least oneinstance of R^(Z) is substituted alkenyl. In certain embodiments, atleast one instance of R^(Z) is unsubstituted alkenyl. In certainembodiments, at least one instance of R^(Z) is substituted alkynyl. Incertain embodiments, at least one instance of R^(Z) is unsubstitutedalkynyl. In certain embodiments, at least one instance of R^(Z) issubstituted or unsubstituted carbocyclyl. In certain embodiments, atleast one instance of R^(Z) is saturated carbocyclyl. In certainembodiments, at least one instance of R^(Z) is unsaturated carbocyclyl.In certain embodiments, at least one instance of R^(Z) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, at least oneinstance of R^(Z) is substituted or unsubstituted heterocyclyl. Incertain embodiments, at least one instance of R^(Z) is saturatedheterocyclyl. In certain embodiments, at least one instance of R^(Z) isunsaturated heterocyclyl. In certain embodiments, at least one instanceof R^(Z) is substituted or unsubstituted, 4- to 7-membered, monocyclicheterocyclyl, wherein one, two, or three atoms in the heterocyclic ringsystem are independently nitrogen, oxygen, or sulfur. In certainembodiments, at least one instance of R^(Z) is substituted orunsubstituted, 6-membered, monocyclic heterocyclyl, wherein one or twoatoms in the heterocyclic ring system are independently nitrogen,oxygen, or sulfur. In certain embodiments, at least one instance ofR^(Z) is of the formula:

In certain embodiments, at least one instance of R^(Z) is of theformula:

In certain embodiments, at least one instance of R^(Z) is of theformula:

In certain embodiments, at least one instance of R^(Z) is of theformula:

In certain embodiments, at least one instance of R^(Z) is of theformula:

In certain embodiments, at least one instance of R^(Z) is substituted orunsubstituted aryl. In certain embodiments, at least one instance ofR^(Z) is 6- to 10-membered aryl. In certain embodiments, at least oneinstance of R^(Z) is monocyclic aryl. In certain embodiments, at leastone instance of R^(Z) is substituted phenyl. In certain embodiments, atleast one instance of R^(Z) is unsubstituted phenyl. In certainembodiments, at least one instance of R^(Z) is bicyclic aryl. In certainembodiments, at least one instance of R^(Z) is substituted orunsubstituted heteroaryl. In certain embodiments, at least one instanceof R^(Z) is heteroaryl, wherein one, two, three, or four atoms in theheteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(Z) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(Z) is 5- or 6-membered,monocyclic heteroaryl. In certain embodiments, at least one instance ofR^(Z) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, R^(Z) is —OR^(Z1). In certain embodiments, R^(Z) is—OH. In certain embodiments, R^(Z) is —OMe. In certain embodiments,R^(Z) is —OEt. In certain embodiments, R^(Z) is —OPr. In certainembodiments, R^(Z) is —OBu. In certain embodiments, R^(Z) is —OBn. Incertain embodiments, R^(Z) is —OPh. In certain embodiments, R^(Z) is—SR^(Z1). In certain embodiments, R^(Z) is —SH. In certain embodiments,R^(Z) is —SMe. In certain embodiments, R^(Z) is —N(R^(Z1))₂. In certainembodiments, R^(Z) is —NH₂. In certain embodiments, R^(Z) is —NHMe. Incertain embodiments, R^(Z) is —NMe₂. In certain embodiments, at leastone instance of R^(Z) is a nitrogen protecting group when attached to anitrogen atom. In certain embodiments, at least one instance of R^(Z) isBn, Boc, Cbz, Fmoc, trifluoroacetyl, triphenylmethyl, acetyl, or Ts whenattached to a nitrogen atom.

In certain embodiments, two instances of R^(Z) are joined to form asubstituted or unsubstituted carbocyclic ring. In certain embodiments,two instances of R^(Z) are joined to form a saturated or unsaturatedcarbocyclic ring. In certain embodiments, two instances of R^(Z) arejoined to form a substituted or unsubstituted, 3- to 7-membered,monocyclic carbocyclic ring. In certain embodiments, two instances ofR^(Z) are joined to form a substituted or unsubstituted heterocyclicring. In certain embodiments, two instances of R^(Z) are joined to forma saturated or unsaturated heterocyclic ring. In certain embodiments,two instances of R^(Z) are joined to form a heterocyclic ring, whereinone, two, or three atoms in the heterocyclic ring system areindependently selected from the group consisting of nitrogen, oxygen,and sulfur. In certain embodiments, two instances of R^(Z) are joined toform a 3- to 7-membered, monocyclic heterocyclic ring.

In certain embodiments, at least one instance of R^(Z1) is H. In certainembodiments, at least one instance of R^(Z1) is substituted acyl. Incertain embodiments, at least one instance of R^(Z1) is unsubstitutedacyl. In certain embodiments, at least one instance of R^(Z1) is acetyl.In certain embodiments, at least one instance of R^(Z1) is substitutedalkyl. In certain embodiments, at least one instance of R^(Z1) isunsubstituted alkyl. In certain embodiments, at least one instance ofR^(Z1) is unsubstituted C₁₋₆ alkyl. In certain embodiments, at least oneinstance of R^(Z1) is methyl. In certain embodiments, at least oneinstance of R^(Z1) is ethyl. In certain embodiments, at least oneinstance of R^(Z1) is propyl. In certain embodiments, at least oneinstance of R^(Z1) is butyl. In certain embodiments, at least oneinstance of R^(Z1) is pentyl. In certain embodiments, at least oneinstance of R^(Z1) is hexyl. In certain embodiments, R^(Z1) issubstituted alkenyl. In certain embodiments, R^(Z1) is unsubstitutedalkenyl. In certain embodiments, R^(Z1) is substituted alkynyl. Incertain embodiments, R^(Z1) is unsubstituted alkynyl. In certainembodiments, at least one instance of R^(Z1) is substituted orunsubstituted carbocyclyl. In certain embodiments, at least one instanceof R^(Z1) is saturated carbocyclyl. In certain embodiments, at least oneinstance of R^(Z1) is unsaturated carbocyclyl. In certain embodiments,at least one instance of R^(Z1) is 3- to 7-membered, monocycliccarbocyclyl. In certain embodiments, at least one instance of R^(Z1) issubstituted or unsubstituted heterocyclyl. In certain embodiments, atleast one instance of R^(Z1) is saturated heterocyclyl. In certainembodiments, at least one instance of R^(Z1) is unsaturatedheterocyclyl. In certain embodiments, at least one instance of R^(Z1) isheterocyclyl, wherein one, two, or three atoms in the heterocyclic ringsystem are independently selected from the group consisting of nitrogen,oxygen, and sulfur. In certain embodiments, at least one instance ofR^(Z1) is 3- to 7-membered, monocyclic heterocyclyl. In certainembodiments, at least one instance of R^(Z1) is substituted orunsubstituted aryl. In certain embodiments, at least one instance ofR^(Z1) is 6- to 10-membered aryl. In certain embodiments, at least oneinstance of R^(Z1) is monocyclic aryl. In certain embodiments, at leastone instance of R^(Z1) is substituted phenyl. In certain embodiments, atleast one instance of R^(Z1) is unsubstituted phenyl. In certainembodiments, at least one instance of R^(Z1) is bicyclic aryl. Incertain embodiments, at least one instance of R^(Z1) is substituted orunsubstituted heteroaryl. In certain embodiments, at least one instanceof R^(Z1) is heteroaryl, wherein one, two, three, or four atoms in theheteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(Z1) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(Z1) is 5- or 6-membered,monocyclic heteroaryl. In certain embodiments, at least one instance ofR^(Z1) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, at least one instance of R^(Z1) is a nitrogenprotecting group when attached to a nitrogen atom. In certainembodiments, at least one instance of R^(Z1) is Bn, Boc, Cbz, Fmoc,trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to anitrogen atom. In certain embodiments, at least one instance of R^(Z1)is an oxygen protecting group when attached to an oxygen atom. Incertain embodiments, at least one instance of R^(Z1) is silyl, TBDPS,TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl, pivaloyl, orbenzoyl when attached to an oxygen atom. In certain embodiments, atleast one instance of R^(Z1) is a sulfur protecting group when attachedto a sulfur atom. In certain embodiments, at least one instance ofR^(Z1) is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl,2-pyridine-sulfenyl, or triphenylmethyl when attached to a sulfur atom.In certain embodiments, two instances of R^(Z1) are joined to form asubstituted or unsubstituted heterocyclic ring. In certain embodiments,two instances of R^(Z1) are joined to form a saturated or unsaturatedheterocyclic ring. In certain embodiments, two instances of R^(Z1) arejoined to form a heterocyclic ring, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, twoinstances of R^(Z1) are joined to form a 3- to 7-membered, monocyclicheterocyclic ring. In certain embodiments, two instances of R^(Z1) arejoined to form a substituted or unsubstituted heteroaryl ring. Incertain embodiments, two instances of R^(Z1) are joined to form asubstituted or unsubstituted, 5- to 6-membered, monocyclic heteroarylring, wherein one, two, three, or four atoms in the heteroaryl ringsystem are independently nitrogen, oxygen, or sulfur.

Formula (I) or (II) may include one or more substituents R^(A). Incertain embodiments, at least two instances of R^(A) are different. Incertain embodiments, all instances of R^(A) are the same. In certainembodiments, at least one instance of R^(A) is H. In certainembodiments, all instances of R^(A) are H. In certain embodiments, atleast one instance of R^(A) is halogen. In certain embodiments, at leastone instance of R^(A) is F. In certain embodiments, at least oneinstance of R^(A) is Cl. In certain embodiments, at least one instanceof R^(A) is Br. In certain embodiments, at least one instance of R^(A)is I (iodine). In certain embodiments, at least one instance of R^(A) issubstituted alkyl. In certain embodiments, at least one instance ofR^(A) is unsubstituted alkyl. In certain embodiments, at least oneinstance of R^(A) is unsubstituted C₁₋₆ alkyl. In certain embodiments,all instances of R^(A) are unsubstituted C₁₋₆ alkyl. In certainembodiments, at least one instance of R^(A) is substituted C₁₋₆ alkyl.In certain embodiments, at least one instance of R^(A) is C₁₋₆ alkylsubstituted with at least one halogen. In certain embodiments, at leastone instance of R^(A) is —CH₃. In certain embodiments, all instances ofR^(A) are —CH₃. In certain embodiments, at least one instance of R^(A)is substituted methyl. In certain embodiments, at least one instance ofR^(A) is —CH₂F. In certain embodiments, at least one instance of R^(A)is —CHF₂. In certain embodiments, at least one instance of R^(A) is—CF₃. In certain embodiments, at least one instance of R^(A) is ethyl.In certain embodiments, at least one instance of R^(A) is propyl. Incertain embodiments, at least one instance of R^(A) is butyl. In certainembodiments, at least one instance of R^(A) is pentyl. In certainembodiments, at least one instance of R^(A) is hexyl. In certainembodiments, at least one instance of R^(A) is substituted alkenyl. Incertain embodiments, at least one instance of R^(A) is unsubstitutedalkenyl. In certain embodiments, at least one instance of R^(A) isunsubstituted alkynyl. In certain embodiments, at least one instance ofR^(A) is unsubstituted alkynyl. In certain embodiments, at least oneinstance of R^(A) is substituted carbocyclyl. In certain embodiments, atleast one instance of R^(A) is unsubstituted carbocyclyl. In certainembodiments, at least one instance of R^(A) is saturated carbocyclyl. Incertain embodiments, at least one instance of R^(A) is unsaturatedcarbocyclyl. In certain embodiments, at least one instance of R^(A) ismonocyclic carbocyclyl. In certain embodiments, at least one instance ofR^(A) is 3- to 7-membered, monocyclic carbocyclyl. In certainembodiments, at least one instance of R^(A) is substituted heterocyclyl.In certain embodiments, at least one instance of R^(A) is unsubstitutedheterocyclyl. In certain embodiments, at least one instance of R^(A) issaturated heterocyclyl. In certain embodiments, at least one instance ofR^(A) is unsaturated heterocyclyl. In certain embodiments, at least oneinstance of R^(A) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(A) is monocyclic heterocyclyl. In certainembodiments, at least one instance of R^(A) is 3- to 7-membered,monocyclic heterocyclyl. In certain embodiments, at least one instanceof R^(A) is substituted aryl. In certain embodiments, at least oneinstance of R^(A) is unsubstituted aryl. In certain embodiments, atleast one instance of R^(A) is 6- to 10-membered aryl. In certainembodiments, at least one instance of R^(A) is substituted phenyl. Incertain embodiments, at least one instance of R^(A) is unsubstitutedphenyl. In certain embodiments, at least one instance of R^(A) issubstituted heteroaryl. In certain embodiments, at least one instance ofR^(A) is unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(A) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(A) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(A) is 5-membered, monocyclicheteroaryl. In certain embodiments, at least one instance of R^(A) is6-membered, monocyclic heteroaryl. In certain embodiments, at least oneinstance of R^(A) is bicyclic heteroaryl, wherein the point ofattachment may be on any atom of the bicyclic heteroaryl ring system, asvalency permits. In certain embodiments, at least one instance of R^(A)is 9- or 10-membered, bicyclic heteroaryl. In certain embodiments, atleast one instance of R^(A) is —OR^(A1). In certain embodiments, atleast one instance of R^(A) is —OH. In certain embodiments, at least oneinstance of R^(A) is —OMe. In certain embodiments, at least one instanceof R^(A) is —OEt. In certain embodiments, at least one instance of R^(A)is —OPr. In certain embodiments, at least one instance of R^(A) is —OBu.In certain embodiments, at least one instance of R^(A) is —OBn. Incertain embodiments, at least one instance of R^(A) is —OPh. In certainembodiments, at least one instance of R^(A) is —SR^(A1). In certainembodiments, at least one instance of R^(A) is —SH. In certainembodiments, at least one instance of R^(A) is —SMe. In certainembodiments, at least one instance of R^(A) is —N(R^(A1))₂. In certainembodiments, at least one instance of R^(A) is —NH₂. In certainembodiments, at least one instance of R^(A) is —NHMe. In certainembodiments, at least one instance of R^(A) is —NMe₂. In certainembodiments, at least one instance of R^(A) is —CN. In certainembodiments, at least one instance of R^(A) is —SCN. In certainembodiments, at least one instance of R^(A) is —C(═NR^(A1))R^(A1),—C(═NR^(A1))OR^(A1), or —C(═NR^(A1))N(R^(A1))₂. In certain embodiments,at least one instance of R^(A) is —C(═O)R^(A1) or —C(═O)OR^(A1). Incertain embodiments, at least one instance of R^(A) is —C(═O)N(R^(A1))₂.In certain embodiments, at least one instance of R^(A) is —C(═O)NMe₂,—C(═O)NHMe, or —C(═O)NH₂. In certain embodiments, at least one instanceof R^(A) is —NO₂. In certain embodiments, at least one instance of R^(A)is —NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), or—NR^(A1)C(═O)N(R^(A1))₂. In certain embodiments, at least one instanceof R^(A) is —OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂.

In certain embodiments, at least one instance of R^(A1) is H. In certainembodiments, at least one instance of R^(A1) is substituted acyl. Incertain embodiments, at least one instance of R^(A1) is unsubstitutedacyl. In certain embodiments, at least one instance of R^(A1) is acetyl.In certain embodiments, at least one instance of R^(A1) is substitutedalkyl. In certain embodiments, at least one instance of R^(A1) isunsubstituted alkyl. In certain embodiments, at least one instance ofR^(A1) is unsubstituted C₁₋₆ alkyl. In certain embodiments, at least oneinstance of R^(A1) is methyl. In certain embodiments, at least oneinstance of R^(A1) is ethyl. In certain embodiments, at least oneinstance of R^(A1) is propyl. In certain embodiments, at least oneinstance of R^(A1) is butyl. In certain embodiments, at least oneinstance of R^(A1) is pentyl. In certain embodiments, at least oneinstance of R^(A1) is hexyl. In certain embodiments, at least oneinstance of R^(A1) is substituted alkenyl. In certain embodiments, atleast one instance of R^(A1) is unsubstituted alkenyl. In certainembodiments, at least one instance of R^(A1) is substituted alkynyl. Incertain embodiments, at least one instance of R^(A1) is unsubstitutedalkynyl. In certain embodiments, at least one instance of R^(A1) issubstituted or unsubstituted carbocyclyl. In certain embodiments, atleast one instance of R^(A1) is saturated carbocyclyl. In certainembodiments, at least one instance of R^(A1) is unsaturated carbocyclyl.In certain embodiments, at least one instance of R^(A1) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, at least oneinstance of R^(A1) is substituted or unsubstituted heterocyclyl. Incertain embodiments, at least one instance of R^(A1) is saturatedheterocyclyl. In certain embodiments, at least one instance of R^(A1) isunsaturated heterocyclyl. In certain embodiments, at least one instanceof R^(A1) is heterocyclyl, wherein one, two, or three atoms in theheterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(A1) is 3- to 7-membered, monocyclicheterocyclyl. In certain embodiments, at least one instance of R^(A1) issubstituted or unsubstituted aryl. In certain embodiments, at least oneinstance of R^(A1) is 6- to 10-membered aryl. In certain embodiments, atleast one instance of R^(A1) is monocyclic aryl. In certain embodiments,at least one instance of R^(A1) is substituted phenyl. In certainembodiments, at least one instance of R^(A1) is unsubstituted phenyl. Incertain embodiments, at least one instance of R^(A1) is bicyclic aryl.In certain embodiments, at least one instance of R^(A1) is substitutedor unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(A1) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(A1) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(A1) is 5- or 6-membered,monocyclic heteroaryl. In certain embodiments, at least one instance ofR^(A1) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, at least one instance of R^(A1) is a nitrogenprotecting group when attached to a nitrogen atom. In certainembodiments, at least one instance of R^(A1) is Bn, Boc, Cbz, Fmoc,trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to anitrogen atom. In certain embodiments, R^(A1) is an oxygen protectinggroup when attached to an oxygen atom. In certain embodiments, R^(A1) issilyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl,pivaloyl, or benzoyl when attached to an oxygen atom. In certainembodiments, R^(A1) is a sulfur protecting group when attached to asulfur atom. In certain embodiments, R^(A1) is acetamidomethyl, t-Bu,3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethylwhen attached to a sulfur atom. In certain embodiments, two instances ofR^(A1) are joined to form a substituted or unsubstituted heterocyclicring. In certain embodiments, two instances of R^(A1) are joined to forma saturated or unsaturated heterocyclic ring. In certain embodiments,two instances of R^(A1) are joined to form a heterocyclic ring, whereinone, two, or three atoms in the heterocyclic ring system areindependently selected from the group consisting of nitrogen, oxygen,and sulfur. In certain embodiments, two instances of R^(A1) are joinedto form a 3- to 7-membered, monocyclic heterocyclic ring. In certainembodiments, two instances of R^(A1) are joined to form a substituted orunsubstituted heteroaryl ring. In certain embodiments, two instances ofR^(A1) are joined to form a substituted or unsubstituted, 5- to6-membered, monocyclic heteroaryl ring, wherein one, two, three, or fouratoms in the heteroaryl ring system are independently nitrogen, oxygen,or sulfur.

In certain embodiments, n is 0. In certain embodiments, n is 1. Incertain embodiments, n is 2. In certain embodiments, n is 3. In certainembodiments, n is 4. In certain embodiments, n is 5. In certainembodiments, n is 6. In certain embodiments, n is 7. In certainembodiments, n is 8.

Formula (I) includes a divalent moiety X. In certain embodiments, X isabsent. In certain embodiments, X is —C(═O)—. In certain embodiments, Xis —C(R^(X))₂—. In certain embodiments, X is —CH(R^(X))—. In certainembodiments, X is —CH₂—.

In certain embodiments, at least one instance of R^(X) is H. In certainembodiments, each instance of R^(X) is H. In certain embodiments, atleast one instance of R^(X) is halogen. In certain embodiments, at leastone instance of R^(X) is F. In certain embodiments, at least oneinstance of R^(X) is Cl. In certain embodiments, at least one instanceof R^(X) is Br. In certain embodiments, at least one instance of R^(X)is I (iodine). In certain embodiments, at least one instance of R^(X) isunsubstituted C₁₋₆ alkyl. In certain embodiments, each instance of R^(X)is unsubstituted C₁₋₆ alkyl. In certain embodiments, at least oneinstance of R^(X) is substituted C₁₋₆ alkyl. In certain embodiments, atleast one instance of R^(X) is C₁₋₆ alkyl substituted with at least onehalogen. In certain embodiments, at least one instance of R^(X) is —CH₃.In certain embodiments, each instance of R^(X) is —CH₃. In certainembodiments, at least one instance of R^(X) is substituted methyl. Incertain embodiments, at least one instance of R^(X) is —CH₂F. In certainembodiments, at least one instance of R^(X) is —CHF₂. In certainembodiments, at least one instance of R^(X) is —CF₃. In certainembodiments, at least one instance of R^(X) is ethyl. In certainembodiments, at least one instance of R^(X) is propyl. In certainembodiments, at least one instance of R^(X) is butyl. In certainembodiments, at least one instance of R^(X) is pentyl. In certainembodiments, at least one instance of R^(X) is hexyl.

Formula (I) or (II) may include one or more substituents R^(B). Incertain embodiments, at least two instances of R^(B) are different. Incertain embodiments, all instances of R^(B) are the same. In certainembodiments, at least one instance of R^(B) is H. In certainembodiments, all instances of R^(B) are H. In certain embodiments, atleast one instance of R^(B) is halogen. In certain embodiments, at leastone instance of R^(B) is F. In certain embodiments, at least oneinstance of R^(B) is Cl. In certain embodiments, at least one instanceof R^(B) is Br. In certain embodiments, at least one instance of R^(B)is I (iodine). In certain embodiments, at least one instance of R^(B) issubstituted alkyl. In certain embodiments, at least one instance ofR^(B) is unsubstituted alkyl. In certain embodiments, at least oneinstance of R^(B) is unsubstituted C₁₋₆ alkyl. In certain embodiments,all instances of R^(B) are unsubstituted C₁₋₆ alkyl. In certainembodiments, at least one instance of R^(B) is substituted C₁₋₆ alkyl.In certain embodiments, at least one instance of R^(B) is C₁₋₆ alkylsubstituted with at least one halogen. In certain embodiments, at leastone instance of R^(B) is —CH₃. In certain embodiments, all instances ofR^(B) are —CH₃. In certain embodiments, at least one instance of R^(B)is substituted methyl. In certain embodiments, at least one instance ofR^(B) is —CH₂F. In certain embodiments, at least one instance of R^(B)is —CHF₂. In certain embodiments, at least one instance of R^(B) is—CF₃. In certain embodiments, at least one instance of R^(B) is ethyl.In certain embodiments, at least one instance of R^(B) is propyl. Incertain embodiments, at least one instance of R^(B) is butyl. In certainembodiments, at least one instance of R^(B) is pentyl. In certainembodiments, at least one instance of R^(B) is hexyl. In certainembodiments, at least one instance of R^(B) is substituted alkenyl. Incertain embodiments, at least one instance of R^(B) is unsubstitutedalkenyl. In certain embodiments, at least one instance of R^(B) issubstituted alkynyl. In certain embodiments, at least one instance ofR^(B) is unsubstituted alkynyl. In certain embodiments, at least oneinstance of R^(B) is substituted carbocyclyl. In certain embodiments, atleast one instance of R^(B) is unsubstituted carbocyclyl. In certainembodiments, at least one instance of R^(B) is saturated carbocyclyl. Incertain embodiments, at least one instance of R^(B) is unsaturatedcarbocyclyl. In certain embodiments, at least one instance of R^(B) ismonocyclic carbocyclyl. In certain embodiments, at least one instance ofR^(B) is 3- to 7-membered, monocyclic carbocyclyl. In certainembodiments, at least one instance of R^(B) is substituted heterocyclyl.In certain embodiments, at least one instance of R^(B) is unsubstitutedheterocyclyl. In certain embodiments, at least one instance of R^(B) issaturated heterocyclyl. In certain embodiments, at least one instance ofR^(B) is unsaturated heterocyclyl. In certain embodiments, at least oneinstance of R^(B) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(B) is monocyclic heterocyclyl. In certainembodiments, at least one instance of R^(B) is 3- to 7-membered,monocyclic heterocyclyl. In certain embodiments, at least one instanceof R^(B) is substituted aryl. In certain embodiments, at least oneinstance of R^(B) is unsubstituted aryl. In certain embodiments, atleast one instance of R^(B) is 6- to 10-membered aryl. In certainembodiments, at least one instance of R^(B) is substituted phenyl. Incertain embodiments, at least one instance of R^(B) is unsubstitutedphenyl. In certain embodiments, at least one instance of R^(B) issubstituted heteroaryl. In certain embodiments, at least one instance ofR^(B) is unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(B) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(B) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(B) is 5-membered, monocyclicheteroaryl. In certain embodiments, at least one instance of R^(B) is6-membered, monocyclic heteroaryl. In certain embodiments, at least oneinstance of R^(B) is bicyclic heteroaryl, wherein the point ofattachment may be on any atom of the bicyclic heteroaryl ring system, asvalency permits. In certain embodiments, at least one instance of R^(B)is 9- or 10-membered, bicyclic heteroaryl. In certain embodiments, atleast one instance of R^(B) is —OR^(B1). In certain embodiments, atleast one instance of R^(B) is —OH. In certain embodiments, at least oneinstance of R^(B) is —OMe. In certain embodiments, at least one instanceof R^(B) is —OEt. In certain embodiments, at least one instance of R^(B)is —OPr. In certain embodiments, at least one instance of R^(B) is —OBu.In certain embodiments, at least one instance of R^(B) is —OBn. Incertain embodiments, at least one instance of R^(B) is —OPh. In certainembodiments, at least one instance of R^(B) is —SR^(B1). In certainembodiments, at least one instance of R^(B) is —SH. In certainembodiments, at least one instance of R^(B) is —SMe. In certainembodiments, at least one instance of R^(B) is —N(R^(B1))₂. In certainembodiments, at least one instance of R^(B) is —NH₂. In certainembodiments, at least one instance of R^(B) is —NHMe. In certainembodiments, at least one instance of R^(B) is —NMe₂. In certainembodiments, at least one instance of R^(B) is —CN. In certainembodiments, at least one instance of R^(B) is —SCN. In certainembodiments, at least one instance of R^(B) is —C(═NR^(B1))R^(B1),—C(═NR^(B1))OR^(B1), or —C(═NR^(B1))N(R^(B1))₂. In certain embodiments,at least one instance of R^(B) is —C(═O)R^(B1) or —C(═O)OR^(B1). Incertain embodiments, at least one instance of R^(B) is —C(═O)N(R^(B1))₂.In certain embodiments, at least one instance of R^(B) is —C(═O)NMe₂,—C(═O)NHMe, or —C(═O)NH₂. In certain embodiments, at least one instanceof R^(B) is —NO₂. In certain embodiments, at least one instance of R^(B)is —NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), or—NR^(B1)C(═O)N(R^(B1))₂. In certain embodiments, at least one instanceof R^(B) is —OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂.

In certain embodiments, at least one instance of R^(B1) is H. In certainembodiments, at least one instance of R^(B1) is substituted acyl. Incertain embodiments, at least one instance of R^(B1) is unsubstitutedacyl. In certain embodiments, at least one instance of R^(B1) is acetyl.In certain embodiments, at least one instance of R^(B1) is substitutedalkyl. In certain embodiments, at least one instance of R^(B1) isunsubstituted alkyl. In certain embodiments, at least one instance ofR^(B1) is unsubstituted C₁₋₆ alkyl. In certain embodiments, at least oneinstance of R^(B1) is methyl. In certain embodiments, at least oneinstance of R^(B1) is ethyl. In certain embodiments, at least oneinstance of R^(B1) is propyl. In certain embodiments, at least oneinstance of R^(B1) is butyl. In certain embodiments, at least oneinstance of R^(B1) is pentyl. In certain embodiments, at least oneinstance of R^(B1) is hexyl. In certain embodiments, at least oneinstance of R^(B1) is substituted alkenyl. In certain embodiments, atleast one instance of R^(B1) is unsubstituted alkenyl. In certainembodiments, at least one instance of R^(B1) is substituted alkynyl. Incertain embodiments, at least one instance of R^(B1) is unsubstitutedalkynyl. In certain embodiments, at least one instance of R^(B1) issubstituted or unsubstituted carbocyclyl. In certain embodiments, atleast one instance of R^(B1) is saturated carbocyclyl. In certainembodiments, at least one instance of R^(B1) is unsaturated carbocyclyl.In certain embodiments, at least one instance of R^(B1) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, at least oneinstance of R^(B1) is substituted or unsubstituted heterocyclyl. Incertain embodiments, at least one instance of R^(B1) is saturatedheterocyclyl. In certain embodiments, at least one instance of R^(B1) isunsaturated heterocyclyl. In certain embodiments, at least one instanceof R^(B1) is heterocyclyl, wherein one, two, or three atoms in theheterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(B1) is 3- to 7-membered, monocyclicheterocyclyl. In certain embodiments, at least one instance of R^(B1) issubstituted or unsubstituted aryl. In certain embodiments, at least oneinstance of R^(B1) is 6- to 10-membered aryl. In certain embodiments, atleast one instance of R^(B1) is monocyclic aryl. In certain embodiments,at least one instance of R^(B1) is substituted phenyl. In certainembodiments, at least one instance of R^(B1) is unsubstituted phenyl. Incertain embodiments, at least one instance of R^(B1) is bicyclic aryl.In certain embodiments, at least one instance of R^(B1) is substitutedor unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(B1) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(B1) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(B1) is 5- or 6-membered,monocyclic heteroaryl. In certain embodiments, at least one instance ofR^(B1) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, at least one instance of R^(B1) is a nitrogenprotecting group when attached to a nitrogen atom. In certainembodiments, at least one instance of R^(B1) is Bn, Boc, Cbz, Fmoc,trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to anitrogen atom. In certain embodiments, R^(B1) is an oxygen protectinggroup when attached to an oxygen atom. In certain embodiments, R^(B1) issilyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl,pivaloyl, or benzoyl when attached to an oxygen atom. In certainembodiments, R^(B1) is a sulfur protecting group when attached to asulfur atom. In certain embodiments, R^(B1) is acetamidomethyl, t-Bu,3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethylwhen attached to a sulfur atom. In certain embodiments, two instances ofR^(B1) are joined to form a substituted or unsubstituted heterocyclicring. In certain embodiments, two instances of R^(B1) are joined to forma saturated or unsaturated heterocyclic ring. In certain embodiments,two instances of R^(B1) are joined to form a heterocyclic ring, whereinone, two, or three atoms in the heterocyclic ring system areindependently selected from the group consisting of nitrogen, oxygen,and sulfur. In certain embodiments, two instances of R^(B1) are joinedto form a 3- to 7-membered, monocyclic heterocyclic ring. In certainembodiments, two instances of R^(B1) are joined to form a substituted orunsubstituted heteroaryl ring. In certain embodiments, two instances ofR^(B1) are joined to form a substituted or unsubstituted, 5- to6-membered, monocyclic heteroaryl ring, wherein one, two, three, or fouratoms in the heteroaryl ring system are independently nitrogen, oxygen,or sulfur.

In certain embodiments, m is 0. In certain embodiments, m is 1. Incertain embodiments, m is 2. In certain embodiments, m is 3. In certainembodiments, m is 4.

Formula (I) or (II) includes substituent R^(C) on a nitrogen atom. Incertain embodiments, R^(C) is H. In certain embodiments, R^(C) isunsubstituted C₁₋₆ alkyl. In certain embodiments, R^(C) is substitutedC₁₋₆ alkyl. In certain embodiments, R^(C) is C₁₋₆ alkyl substituted withat least one halogen. In certain embodiments, R^(C) is —CH₃. In certainembodiments, R^(C) is substituted methyl. In certain embodiments, R^(C)is —CH₂F. In certain embodiments, R^(C) is —CHF₂. In certainembodiments, R^(C) is —CF₃. In certain embodiments, R^(C) is ethyl. Incertain embodiments, R^(C) is propyl. In certain embodiments, R^(C) isbutyl. In certain embodiments, R^(C) is pentyl. In certain embodiments,R^(C) is hexyl.

Formula (I) or (II) includes substituent R^(D) on a pyrimidinyl ring. Incertain embodiments, R^(D) is H. In certain embodiments, R^(D) isunsubstituted alkyl. In certain embodiments, R^(D) is substituted alkyl.In certain embodiments, R^(D) is unsubstituted C₁₋₆ alkyl. In certainembodiments, R^(D) is substituted C₁₋₆ alkyl. In certain embodiments,R^(D) is C₁₋₆ alkyl substituted with at least one halogen. In certainembodiments, R^(D) is —CH₃. In certain embodiments, R^(D) is substitutedmethyl. In certain embodiments, R^(D) is —CH₂F. In certain embodiments,R^(D) is —CHF₂. In certain embodiments, R^(D) is —CF₃. In certainembodiments, R^(D) is ethyl. In certain embodiments, R^(D) is propyl. Incertain embodiments, R^(D) is butyl. In certain embodiments, R^(D) ispentyl. In certain embodiments, R^(D) is hexyl.

Formula (I) or (II) includes substituent R^(E) on a nitrogen atom. Incertain embodiments, R^(E) is H. In certain embodiments, R^(E) isunsubstituted alkyl. In certain embodiments, R^(E) is substituted alkyl.In certain embodiments, R^(E) is unsubstituted C₁₋₆ alkyl. In certainembodiments, R^(E) is substituted C₁₋₆ alkyl. In certain embodiments,R^(E) is C₁₋₆ alkyl substituted with at least one halogen. In certainembodiments, R^(E) is —CH₃. In certain embodiments, R^(E) is substitutedmethyl. In certain embodiments, R^(E) is —CH₂F. In certain embodiments,R^(E) is —CHF₂. In certain embodiments, R^(E) is —CF₃. In certainembodiments, R^(E) is ethyl. In certain embodiments, R^(E) is propyl. Incertain embodiments, R^(E) is butyl. In certain embodiments, R^(E) ispentyl. In certain embodiments, R^(E) is hexyl.

Formula (I) or (II) includes substituent R^(F) on a nitrogen atom. Incertain embodiments, R^(F) is H. In certain embodiments, R issubstituted alkyl. In certain embodiments, R^(F) is unsubstituted alkyl.In certain embodiments, R^(F) is unsubstituted C₁₋₆ alkyl. In certainembodiments, R is substituted C₁₋₆ alkyl. In certain embodiments, R^(F)is C₁₋₆ alkyl substituted with at least one halogen. In certainembodiments, R^(F) is —CH₃. In certain embodiments, R^(F) is substitutedmethyl. In certain embodiments, R^(F) is —CH₂F. In certain embodiments,R^(F) is —CHF₂. In certain embodiments, R^(F) is —CF₃. In certainembodiments, R^(F) is ethyl. In certain embodiments, R^(F) is propyl. Incertain embodiments, R^(F) is butyl. In certain embodiments, R^(F) ispentyl. In certain embodiments, R^(F) is hexyl. In certain embodiments,R^(F) is substituted alkenyl. In certain embodiments, R^(F) isunsubstituted alkenyl. In certain embodiments, R is substitutedcarbocyclyl. In certain embodiments, R^(F) is unsubstituted carbocyclyl.In certain embodiments, R^(F) is saturated carbocyclyl. In certainembodiments, R^(F) is unsaturated carbocyclyl. In certain embodiments,R^(F) is monocyclic carbocyclyl. In certain embodiments, R^(F) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, R^(F) issubstituted heterocyclyl. In certain embodiments, R^(F) is unsubstitutedheterocyclyl. In certain embodiments, R^(F) is saturated heterocyclyl.In certain embodiments, R^(F) is unsaturated heterocyclyl. In certainembodiments, R^(F) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments,R^(F) is monocyclic heterocyclyl. In certain embodiments, R^(F) is 3- to7-membered, monocyclic heterocyclyl. In certain embodiments, R^(F) issubstituted aryl. In certain embodiments, R^(F) is unsubstituted aryl.In certain embodiments, R^(F) is 6- to 10-membered aryl. In certainembodiments, R^(F) is substituted phenyl. In certain embodiments, R^(F)is unsubstituted phenyl. In certain embodiments, R^(F) is substitutedheteroaryl. In certain embodiments, R^(F) is unsubstituted heteroaryl.In certain embodiments, R^(F) is heteroaryl, wherein one, two, three, orfour atoms in the heteroaryl ring system are independently selected fromthe group consisting of nitrogen, oxygen, and sulfur. In certainembodiments, R^(F) is monocyclic heteroaryl. In certain embodiments,R^(F) is 5-membered, monocyclic heteroaryl. In certain embodiments,R^(F) is 6-membered, monocyclic heteroaryl. In certain embodiments,R^(F) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, R^(F) is 9- or 10-membered, bicyclic heteroaryl.

Formula (I) or (II) includes substituent R^(G). In certain embodiments,R^(G) is H. In certain embodiments, R^(G) is substituted alkyl. Incertain embodiments, R^(G) is unsubstituted alkyl. In certainembodiments, R^(G) is unsubstituted C₁₋₆ alkyl. In certain embodiments,R^(G) is substituted C₁₋₆ alkyl. In certain embodiments, R^(G) is C₁₋₆alkyl substituted with at least one halogen. In certain embodiments,R^(G) is —CH₃. In certain embodiments, R^(G) is substituted methyl. Incertain embodiments, R^(G) is —CH₂F. In certain embodiments, R^(G) is—CHF₂. In certain embodiments, R^(G) is —CF₃. In certain embodiments,R^(G) is ethyl. In certain embodiments, R^(G) is propyl. In certainembodiments, R^(G) is butyl. In certain embodiments, R^(G) is pentyl. Incertain embodiments, R^(G) is hexyl. In certain embodiments, R^(G) issubstituted alkenyl. In certain embodiments, R^(G) is unsubstitutedalkenyl. In certain embodiments, R^(G) is substituted carbocyclyl. Incertain embodiments, R^(G) is unsubstituted carbocyclyl. In certainembodiments, R^(G) is saturated carbocyclyl. In certain embodiments,R^(G) is unsaturated carbocyclyl. In certain embodiments, R^(G) ismonocyclic carbocyclyl. In certain embodiments, R^(G) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, R^(G) issubstituted heterocyclyl. In certain embodiments, R^(G) is unsubstitutedheterocyclyl. In certain embodiments, R^(G) is saturated heterocyclyl.In certain embodiments, R^(G) is unsaturated heterocyclyl. In certainembodiments, R^(G) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments,R^(G) is monocyclic heterocyclyl. In certain embodiments, R^(G) is 3- to7-membered, monocyclic heterocyclyl. In certain embodiments, R^(G) issubstituted aryl. In certain embodiments, R^(G) is unsubstituted aryl.In certain embodiments, R^(G) is 6- to 10-membered aryl. In certainembodiments, R^(G) is substituted phenyl. In certain embodiments, R^(G)is unsubstituted phenyl. In certain embodiments, R^(G) is substitutedheteroaryl. In certain embodiments, R^(G) is unsubstituted heteroaryl.In certain embodiments, R^(G) is heteroaryl, wherein one, two, three, orfour atoms in the heteroaryl ring system are independently selected fromthe group consisting of nitrogen, oxygen, and sulfur. In certainembodiments, R^(G) is monocyclic heteroaryl. In certain embodiments,R^(G) is 5-membered, monocyclic heteroaryl. In certain embodiments,R^(G) is 6-membered, monocyclic heteroaryl. In certain embodiments,R^(G) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, R^(G) is 9- or 10-membered, bicyclic heteroaryl.

Formula (I) or (II) includes substituent R^(H). In certain embodiments,R^(H) is H. In certain embodiments, R^(H) is substituted alkyl. Incertain embodiments, R^(H) is unsubstituted alkyl. In certainembodiments, R^(H) is unsubstituted C₁₋₆ alkyl. In certain embodiments,R^(H) is substituted C₁₋₆ alkyl. In certain embodiments, R^(H) is C₁₋₆alkyl substituted with at least one halogen. In certain embodiments,R^(H) is —CH₃. In certain embodiments, R^(H) is substituted methyl. Incertain embodiments, R^(H) is —CH₂F. In certain embodiments, R^(H) is—CHF₂. In certain embodiments, R^(H) is —CF₃. In certain embodiments,R^(H) is ethyl. In certain embodiments, R^(H) is propyl. In certainembodiments, R^(H) is butyl. In certain embodiments, R^(H) is pentyl. Incertain embodiments, R^(H) is hexyl. In certain embodiments, R^(H) issubstituted alkenyl. In certain embodiments, R^(H) is unsubstitutedalkenyl. In certain embodiments, R^(H) is substituted carbocyclyl. Incertain embodiments, R^(H) is unsubstituted carbocyclyl. In certainembodiments, R^(H) is saturated carbocyclyl. In certain embodiments,R^(H) is unsaturated carbocyclyl. In certain embodiments, R^(H) ismonocyclic carbocyclyl. In certain embodiments, R^(H) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, R^(H) issubstituted heterocyclyl. In certain embodiments, R^(H) is unsubstitutedheterocyclyl. In certain embodiments, R^(H) is saturated heterocyclyl.In certain embodiments, R^(H) is unsaturated heterocyclyl. In certainembodiments, R^(H) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments,R^(H) is monocyclic heterocyclyl. In certain embodiments, R^(H) is 3- to7-membered, monocyclic heterocyclyl. In certain embodiments, R^(H) issubstituted aryl. In certain embodiments, R^(H) is unsubstituted aryl.In certain embodiments, R^(H) is 6- to 10-membered aryl. In certainembodiments, R^(H) is substituted phenyl. In certain embodiments, R^(H)is unsubstituted phenyl. In certain embodiments, R^(H) is substitutedheteroaryl. In certain embodiments, R^(H) is unsubstituted heteroaryl.In certain embodiments, R^(H) is heteroaryl, wherein one, two, three, orfour atoms in the heteroaryl ring system are independently selected fromthe group consisting of nitrogen, oxygen, and sulfur. In certainembodiments, R^(H) is monocyclic heteroaryl. In certain embodiments,R^(H) is 5-membered, monocyclic heteroaryl. In certain embodiments,R^(H) is 6-membered, monocyclic heteroaryl. In certain embodiments,R^(H) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, R^(H) is 9- or 10-membered, bicyclic heteroaryl.

In certain embodiments, each of R^(G) and R^(H) is hydrogen.

In certain embodiments, R^(G) and R^(H) are joined to form a substitutedphenyl ring. In certain embodiments, R^(G) and R^(H) are joined to forman unsubstituted phenyl ring. In certain embodiments, a compounddescribed herein is of Formula (II-A):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof, wherein:

each instance of R^(J) is independently hydrogen, halogen, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, —OR^(J1),—N(R^(J1))₂, —SR^(J1), —CN, —SCN, —C(═NR^(J1))R^(J1),—C(═NR^(J1))OR^(J1), —C(═NR^(J1))N(R^(J1))₂, —C(═O)R^(J1),—C(═O)OR^(J1), —C(═O)N(R^(J1))₂, —NO₂, —NR^(J1)C(═O)R^(J1),—NR^(J1)C(═O)OR^(J1), —NR^(J1)C(═O)N(R^(J1))₂, —OC(═O)R^(J1),—OC(═O)OR^(J1), or —OC(═O)N(R^(J1))₂, wherein each instance of R^(J1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, a nitrogenprotecting group when attached to a nitrogen atom, an oxygen protectinggroup when attached to an oxygen atom, or a sulfur protecting group whenattached to a sulfur atom, or two R^(J1) groups are joined to form asubstituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; and

k is 0, 1, 2, 3, or 4.

In certain embodiments, a compound described herein is of Formula (I-A):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

Formula (I-A) or (II-A) may include one or more substituents R^(J). Incertain embodiments, at least two instances of R^(J) are different. Incertain embodiments, all instances of R^(J) are the same. In certainembodiments, at least one instance of R^(J) is H. In certainembodiments, all instances of R^(J) are H. In certain embodiments, atleast one instance of R^(J) is halogen. In certain embodiments, at leastone instance of R^(J) is F. In certain embodiments, at least oneinstance of R^(J) is Cl. In certain embodiments, at least one instanceof R^(J) is Br. In certain embodiments, at least one instance of R^(J)is I (iodine). In certain embodiments, at least one instance of R^(J) issubstituted alkyl. In certain embodiments, at least one instance ofR^(J) is unsubstituted alkyl. In certain embodiments, at least oneinstance of R^(J) is unsubstituted C₁₋₆ alkyl. In certain embodiments,all instances of R^(J) are unsubstituted C₁₋₆ alkyl. In certainembodiments, at least one instance of R^(J) is substituted C₁₋₆ alkyl.In certain embodiments, at least one instance of R^(J) is C₁₋₆ alkylsubstituted with at least one halogen. In certain embodiments, at leastone instance of R^(J) is —CH₃. In certain embodiments, all instances ofR^(J) are —CH₃. In certain embodiments, at least one instance of R^(J)is substituted methyl. In certain embodiments, at least one instance ofR^(J) is —CH₂F. In certain embodiments, at least one instance of R^(J)is —CHF₂. In certain embodiments, at least one instance of R^(J) is—CF₃. In certain embodiments, at least one instance of R^(J) is ethyl.In certain embodiments, at least one instance of R^(J) is propyl. Incertain embodiments, at least one instance of R^(J) is butyl. In certainembodiments, at least one instance of R^(J) is pentyl. In certainembodiments, at least one instance of R^(J) is hexyl. In certainembodiments, at least one instance of R^(J) is substituted alkenyl. Incertain embodiments, at least one instance of R^(J) is unsubstitutedalkenyl. In certain embodiments, at least one instance of R^(J) issubstituted alkynyl. In certain embodiments, at least one instance ofR^(J) is unsubstituted alkynyl. In certain embodiments, at least oneinstance of R^(J) is substituted carbocyclyl. In certain embodiments, atleast one instance of R^(J) is unsubstituted carbocyclyl. In certainembodiments, at least one instance of R^(J) is saturated carbocyclyl. Incertain embodiments, at least one instance of R^(J) is unsaturatedcarbocyclyl. In certain embodiments, at least one instance of R^(J) ismonocyclic carbocyclyl. In certain embodiments, at least one instance ofR^(J) is 3- to 7-membered, monocyclic carbocyclyl. In certainembodiments, at least one instance of R^(J) is substituted heterocyclyl.In certain embodiments, at least one instance of R^(J) is unsubstitutedheterocyclyl. In certain embodiments, at least one instance of R^(J) issaturated heterocyclyl. In certain embodiments, at least one instance ofR^(J) is unsaturated heterocyclyl. In certain embodiments, at least oneinstance of R^(J) is heterocyclyl, wherein one, two, or three atoms inthe heterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(J) is monocyclic heterocyclyl. In certainembodiments, at least one instance of R^(J) is 3- to 7-membered,monocyclic heterocyclyl. In certain embodiments, at least one instanceof R^(J) is substituted aryl. In certain embodiments, at least oneinstance of R^(J) is unsubstituted aryl. In certain embodiments, atleast one instance of R^(J) is 6- to 10-membered aryl. In certainembodiments, at least one instance of R^(J) is substituted phenyl. Incertain embodiments, at least one instance of R^(J) is unsubstitutedphenyl. In certain embodiments, at least one instance of R^(J) issubstituted heteroaryl. In certain embodiments, at least one instance ofR^(J) is unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(J) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(J) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(J) is 5-membered, monocyclicheteroaryl. In certain embodiments, at least one instance of R^(J) is6-membered, monocyclic heteroaryl. In certain embodiments, at least oneinstance of R^(J) is bicyclic heteroaryl, wherein the point ofattachment may be on any atom of the bicyclic heteroaryl ring system, asvalency permits. In certain embodiments, at least one instance of R^(J)is 9- or 10-membered, bicyclic heteroaryl. In certain embodiments, atleast one instance of R^(J) is —OR^(J1). In certain embodiments, atleast one instance of R^(J) is —OH. In certain embodiments, at least oneinstance of R^(J) is —OMe. In certain embodiments, at least one instanceof R^(J) is —OEt. In certain embodiments, at least one instance of R^(J)is —OPr. In certain embodiments, at least one instance of R^(J) is —OBu.In certain embodiments, at least one instance of R^(J) is —OBn. Incertain embodiments, at least one instance of R^(J) is —OPh. In certainembodiments, at least one instance of R^(J) is —SR^(J1). In certainembodiments, at least one instance of R^(J) is —SH. In certainembodiments, at least one instance of R^(J) is —SMe. In certainembodiments, at least one instance of R^(J) is —N(R^(J1))₂. In certainembodiments, at least one instance of R^(J) is —NH₂. In certainembodiments, at least one instance of R^(J) is —NHMe. In certainembodiments, at least one instance of R^(J) is —NMe₂. In certainembodiments, at least one instance of R^(J) is —CN. In certainembodiments, at least one instance of R^(J) is —SCN. In certainembodiments, at least one instance of R^(J) is —C(═NR^(J1))R^(J1),—C(═NR^(J1))OR^(J1), or —C(═NR^(J1))N(R^(J1))₂. In certain embodiments,at least one instance of R^(J) is —C(═O)R^(J1) or —C(═O)OR^(J1). Incertain embodiments, at least one instance of R^(J) is —C(═O)N(R^(J1))₂.In certain embodiments, at least one instance of R^(J) is —C(═O)NMe₂,—C(═O)NHMe, or —C(═O)NH₂. In certain embodiments, at least one instanceof R^(J) is —NO₂. In certain embodiments, at least one instance of R^(J)is —NR^(J1)C(═O)R^(J1), —NR^(J1)C(═O)OR^(J1), or—NR^(J1)C(═O)N(R^(J1))₂. In certain embodiments, at least one instanceof R^(J) is —OC(═O)R^(J1), —OC(═O)OR^(J1), or —OC(═O)N(R^(J1))₂.

In certain embodiments, at least one instance of R^(J1) is H. In certainembodiments, at least one instance of R^(J1) is substituted acyl. Incertain embodiments, at least one instance of R^(J1) is unsubstitutedacyl. In certain embodiments, at least one instance of R^(J1) is acetyl.In certain embodiments, at least one instance of R^(J1) is substitutedalkyl. In certain embodiments, at least one instance of R^(J1) isunsubstituted alkyl. In certain embodiments, at least one instance ofR^(J1) is unsubstituted C₁₋₆ alkyl. In certain embodiments, at least oneinstance of R^(J1) is methyl. In certain embodiments, at least oneinstance of R^(J1) is ethyl. In certain embodiments, at least oneinstance of R^(J1) is propyl. In certain embodiments, at least oneinstance of R^(J1) is butyl. In certain embodiments, at least oneinstance of R^(J1) is pentyl. In certain embodiments, at least oneinstance of R^(J1) is hexyl. In certain embodiments, at least oneinstance of R^(J1) is substituted alkenyl. In certain embodiments, atleast one instance of R^(J1) is unsubstituted alkenyl. In certainembodiments, at least one instance of R^(J1) is substituted alkynyl. Incertain embodiments, at least one instance of R^(J1) is unsubstitutedalkynyl. In certain embodiments, at least one instance of R^(J1) issubstituted or unsubstituted carbocyclyl. In certain embodiments, atleast one instance of R^(J1) is saturated carbocyclyl. In certainembodiments, at least one instance of R^(J1) is unsaturated carbocyclyl.In certain embodiments, at least one instance of R^(J1) is 3- to7-membered, monocyclic carbocyclyl. In certain embodiments, at least oneinstance of R^(J1) is substituted or unsubstituted heterocyclyl. Incertain embodiments, at least one instance of R^(J1) is saturatedheterocyclyl. In certain embodiments, at least one instance of R^(J1) isunsaturated heterocyclyl. In certain embodiments, at least one instanceof R^(J1) is heterocyclyl, wherein one, two, or three atoms in theheterocyclic ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(J1) is 3- to 7-membered, monocyclicheterocyclyl. In certain embodiments, at least one instance of R^(J1) issubstituted or unsubstituted aryl. In certain embodiments, at least oneinstance of R^(J1) is 6- to 10-membered aryl. In certain embodiments, atleast one instance of R^(J1) is monocyclic aryl. In certain embodiments,at least one instance of R^(J1) is substituted phenyl. In certainembodiments, at least one instance of R^(J1) is unsubstituted phenyl. Incertain embodiments, at least one instance of R^(J1) is bicyclic aryl.In certain embodiments, at least one instance of R^(J1) is substitutedor unsubstituted heteroaryl. In certain embodiments, at least oneinstance of R^(J1) is heteroaryl, wherein one, two, three, or four atomsin the heteroaryl ring system are independently selected from the groupconsisting of nitrogen, oxygen, and sulfur. In certain embodiments, atleast one instance of R^(J1) is monocyclic heteroaryl. In certainembodiments, at least one instance of R^(J1) is 5- or 6-membered,monocyclic heteroaryl. In certain embodiments, at least one instance ofR^(J1) is bicyclic heteroaryl, wherein the point of attachment may be onany atom of the bicyclic heteroaryl ring system, as valency permits. Incertain embodiments, at least one instance of R^(J1) is a nitrogenprotecting group when attached to a nitrogen atom. In certainembodiments, at least one instance of R^(J1) is Bn, Boc, Cbz, Fmoc,trifluoroacetyl, triphenylmethyl, acetyl, or Ts when attached to anitrogen atom. In certain embodiments, R^(J1) is an oxygen protectinggroup when attached to an oxygen atom. In certain embodiments, R^(J1) issilyl, TBDPS, TBDMS, TIPS, TES, TMS, MOM, THP, t-Bu, Bn, allyl, acetyl,pivaloyl, or benzoyl when attached to an oxygen atom. In certainembodiments, R^(J1) is a sulfur protecting group when attached to asulfur atom. In certain embodiments, R^(J1) is acetamidomethyl, t-Bu,3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethylwhen attached to a sulfur atom. In certain embodiments, two instances ofR^(J1) are joined to form a substituted or unsubstituted heterocyclicring. In certain embodiments, two instances of R^(J1) are joined to forma saturated or unsaturated heterocyclic ring. In certain embodiments,two instances of R^(J1) are joined to form a heterocyclic ring, whereinone, two, or three atoms in the heterocyclic ring system areindependently selected from the group consisting of nitrogen, oxygen,and sulfur. In certain embodiments, two instances of R^(J1) are joinedto form a 3- to 7-membered, monocyclic heterocyclic ring. In certainembodiments, two instances of R^(J1) are joined to form a substituted orunsubstituted heteroaryl ring. In certain embodiments, two instances ofR^(J1) are joined to form a substituted or unsubstituted, 5- to6-membered, monocyclic heteroaryl ring, wherein one, two, three, or fouratoms in the heteroaryl ring system are independently nitrogen, oxygen,or sulfur.

In certain embodiments, k is 0. In certain embodiments, k is 1. Incertain embodiments, k is 2. In certain embodiments, k is 3. In certainembodiments, k is 4.

In certain embodiments, a compound described herein is of Formula(II-B):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of Formula (I-B):

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt, solvate, hydrate, polymorph,co-crystal, tautomer, stereoisomer, isotopically labeled derivative, orprodrug thereof.

In certain embodiments, a compound described herein is of the formula:

or a pharmaceutically acceptable salt (e.g., a trifluoroacetic acid salt(compound 2-075)), solvate, hydrate, polymorph, co-crystal, tautomer,stereoisomer, isotopically labeled derivative, or prodrug thereof.

In certain embodiments, the compounds described herein are compounds ofFormula (II), and pharmaceutically acceptable salts, solvates, hydrates,polymorphs, co-crystals, tautomers, stereoisomers, isotopically labeledderivatives, and prodrugs thereof. In certain embodiments, the compoundsdescribed herein are compounds of Formula (II), and pharmaceuticallyacceptable salts, solvates, and hydrates thereof. In certainembodiments, the compounds described herein are compounds of Formula(II), and pharmaceutically acceptable salts thereof. In certainembodiments, the compounds described herein are compounds of Formula(II). In certain embodiments, the compounds described herein arecompounds of Formula (I), and pharmaceutically acceptable salts,solvates, hydrates, polymorphs, co-crystals, tautomers, stereoisomers,isotopically labeled derivatives, and prodrugs thereof. In certainembodiments, the compounds described herein are compounds of Formula(I), and pharmaceutically acceptable salts, solvates, and hydratesthereof. In certain embodiments, the compounds described herein arecompounds of Formula (I), and pharmaceutically acceptable salts thereof.In certain embodiments, the compounds described herein are compounds ofFormula (I).

Compounds described herein are binders of bromodomain-containingproteins. In certain embodiments, the compounds described herein bind toa bromodomain-containing protein. Without wishing to be bound by anyparticular theory, the compounds described herein are thought to bind ina binding pocket of a bromodomain of a bromodomain-containing protein.In certain embodiments, the compounds described herein bind to thebinding pocket of the bromodomain by mimicking the contact between anacetyl-lysine residue of a second protein (e.g., a histone) and thebinding pocket. In certain embodiments, the compounds described hereinbind to the binding pocket of the bromodomain. In certain embodiments,the compounds described herein covalently bind to thebromodomain-containing protein. In certain embodiments, the compoundsdescribed herein non-covalently bind to the bromodomain-containingprotein. In certain embodiments, the compounds described hereinreversibly bind to the bromodomain-containing protein. In certainembodiments, the compounds described herein non-reversibly bind to thebromodomain-containing protein. In certain embodiments, the compoundsdescribed herein inhibit the activity of a bromodomain-containingprotein. In certain embodiments, the compounds described herein inhibitthe activity of a bromodomain-containing protein because of the bindingof the compound to the bromodomain-containing protein. In certainembodiments, the compounds described herein inhibit the activity of abromodomain-containing protein because of the binding of the compoundsto a bromodomain of the bromodomain-containing protein. In certainembodiments, the compounds described herein inhibit the activity of abromodomain. In certain embodiments, the activity of a bromodomain isthe activity of bromodomain in binding an acetylated lysine residue(e.g., an acetylated lysine residue on the N-terminal tails ofhistones). In certain embodiments, the compounds described hereinspecifically bind to a bromodomain-containing protein. In certainembodiments, the compounds described herein specifically bind to abromodomain of a bromodomain-containing protein. In certain embodiments,the compounds described herein that specifically bind to abromodomain-containing protein show a greater binding affinity to thebromodomain-containing protein than to one or more other proteins or oneor more other bromodomain-containing proteins. In certain embodiments,the compounds described herein non-specifically bind to abromodomain-containing protein. In certain embodiments, the compoundsdescribed herein non-specifically bind to a bromodomain of abromodomain-containing protein. In certain embodiments, the compoundsdescribed herein reduce transcriptional elongation. In certainembodiments, the compounds described herein disrupt the subcellularlocalization of a bromodomain-containing protein. In certainembodiments, the compounds described herein reduce chromatin binding. Incertain embodiments, the compounds described herein inhibit the bindingof Histone H4 Kac peptide to a bromodomain of a bromodomain-containingprotein. In certain embodiments, the compounds described herein form oneor more hydrogen bonds with an evolutionarily conserved asparagine in abromodomain of a bromodomain-containing protein. In certain embodiments,the asparagine is Asn140 in BRD4(1) and Asn429 in BRD2(2). In certainembodiments, the bromodomain-containing protein is BRD4 or BRD2; and theasparagine is Asn140 in BRD4(1) and Asn429 in BRD2(2). In certainembodiments, the compounds described herein bind competitively withchromatin in a cellular environment. It is thus expected that thecompounds described herein may be useful in the treatment of a diseaseassociated with the activity a bromodomain-containing protein (e.g., aproliferative disease).

The bromodomain-containing proteins that may be bound, and/or whoseactivity may be inhibited, by the compounds described herein include,but are not limited to, the bromodomain-containing proteins describedherein. In certain embodiments, the bromodomain-containing protein is abromo and extra terminal (BET) protein. In certain embodiments, thebromodomain-containing protein is BRD2. In certain embodiments, thebromodomain-containing protein is BRD2(1). In certain embodiments, thebromodomain-containing protein is BRD2(2). In certain embodiments, thebromodomain-containing protein is BRD3. In certain embodiments, thebromodomain-containing protein is BRD3(1). In certain embodiments, thebromodomain-containing protein is BRD3(2). In certain embodiments, thebromodomain-containing protein is BRD4. In certain embodiments, thebromodomain-containing protein is BRD4(1). In certain embodiments, thebromodomain-containing protein is BRD4(2). In certain embodiments, thebromodomain-containing protein is BRDT. In certain embodiments, thebromodomain-containing protein is BRDT(1). In certain embodiments, thebromodomain-containing protein is BRDT(2). In certain embodiments, thebromodomain-containing protein is a TBP (TATA box bindingprotein)-associated factor protein (TAF). In certain embodiments, thebromodomain-containing protein is TAF1. In certain embodiments, thebromodomain-containing protein is TAF1L. In certain embodiments, thebromodomain-containing protein is CREB-binding protein (CBP). In certainembodiments, the bromodomain-containing protein is E1A binding proteinp300 (EP300).

The binding affinity of a compound described herein to abromodomain-containing protein may be measured by the dissociationconstant (K_(d)) value of an adduct of the compound described herein andthe bromodomain-containing protein using methods known in the art (e.g.,isothermal titration calorimetry (ITC)). In certain embodiments, theadduct comprises the compound described herein and thebromodomain-containing protein, which are bound (e.g., covalently ornon-covalently) to each other. In certain embodiments, the K_(d) valueof the adduct is at most about 100 μM, at most about 30 μM, at mostabout 10 μM, at most about 3 μM, at most about 1 μM, at most about 300nM, at most about 100 nM, at most about 30 nM, at most about 10 nM, atmost about 3 nM, or at most about 1 nM. In certain embodiments, theK_(d) value of the adduct is at least about 1 nM, at least about 10 nM,at least about 100 nM, at least about 1 μM, at least about 10 μM, or atleast about 100 μM. Combinations of the above-referenced ranges (e.g.,at most about 10 μM and at least about 1 nM) are also within the scopeof the invention. Other ranges are also possible. In certainembodiments, the K_(d) value of the adduct is at most about 10 μM. Incertain embodiments, the K_(d) value of the adduct is at most about 300nM. In certain embodiments, the K_(d) value of the adduct is at mostabout 100 nM.

In certain embodiments, the activity of the bromodomain-containingproteins described herein is inhibited by the compounds describedherein. The inhibition of the activity of a bromodomain-containingprotein by a compound described herein may be measured by the halfmaximal inhibitory concentration (IC₅₀) value of a compound describedherein when the compound described herein, or a pharmaceuticalcomposition thereof, is contacted, directly or indirectly, with thebromodomain-containing protein. The IC₅₀ values may be obtained usingmethods known in the art. In certain embodiments, IC₅₀ values areobtained by a competition binding assay. In certain embodiments, IC₅₀values are obtained by a method described herein. In certainembodiments, the IC₅₀ value of a compound described herein is at mostabout 1 mM, at most about 300 μM, at most about 100 μM, at most about 30μM, at most about 10 μM, at most about 3 μM, at most about 1 μM, at mostabout 300 nM, at most about 100 nM, at most about 30 nM, at most about10 nM, at most about 3 nM, or at most about 1 nM. In certainembodiments, the IC₅₀ value of a compound described herein is at leastabout 1 nM, at least about 3 nM, at least about 10 nM, at least about 30nM, at least about 100 nM, at least about 300 nM, at least about 1 μM,at least about 3 μM, at least about 10 μM, at least about 30 μM, atleast about 100 μM, at least about 300 μM, or at least 1 mM.Combinations of the above-referenced ranges (e.g., at most about 300 μMand at least about 1 μM) are also within the scope of the invention.Other ranges are also possible. In certain embodiments, the IC₅₀ valueof a compound described herein is at most about 300 μM. In certainembodiments, the IC₅₀ value of a compound described herein is at mostabout 30 μM. In certain embodiments, the IC₅₀ value of a compounddescribed herein is at most about 10 μM.

The compounds described herein may selectively inhibit the activity of abromodomain-containing protein. It is understood that, when a compound,pharmaceutical composition, method, use, or kit is referred to as“selectively” inhibiting the activity of a first protein, the compound,pharmaceutical composition, method, use, or kit inhibits the activity ofthe first protein to a greater extent than of at least a second proteinthat is different from the first protein. In certain embodiments, thecompounds described herein selectively inhibit the activity of abromodomain-containing protein, compared to a differentbromodomain-containing protein. In certain embodiments, the compoundsdescribed herein selectively inhibit the activity of abromodomain-containing protein, compared to a protein that is not abromodomain-containing protein. In certain embodiments, the compoundsdescribed herein selectively inhibit the activity of abromodomain-containing protein, compared to a kinase (e.g., a kinasedescribed herein). In certain embodiments, the compounds describedherein selectively inhibit the activity of a bromodomain-containingprotein, compared to MPS1 (TTK), ERK5 (BMK1, MAPK7), a polo kinase(e.g., polo kinase 1, polo kinase 2, polo kinase 3, polo kinase 4),Ack1, Ack2, AbI, DCAMKL1, ABL1, an AbI mutant, DCAMKL2, ARK5, BRK,MKNK2, FGFR4, TNK1, PLK1, ULK2, PLK4, PRKD1, PRKD2, PRKD3, ROS 1,RPS6KA6, TAOK1, TAOK3, TNK2, Bcr-Abl, GAK, cSrc, TPR-Met, Tie2, MET,FGFR3, Aurora, AxI, Bmx, BTK, c-kit, CHK2, Flt3, MST2, p70S6K, PDGFR,PKB, PKC, Raf, ROCK-H, Rsk1, SGK, TrkA, TrkB, and/or TrkC. In certainembodiments, the compounds described herein selectively inhibit theactivity of a bromodomain-containing protein, compared to a MAP kinase.In certain embodiments, the compounds described herein selectivelyinhibit the activity of a bromodomain-containing protein, compared to amitotic spindle kinase. In certain embodiments, the compounds describedherein selectively inhibit the activity of a bromodomain-containingprotein, compared to a polo kinase. In certain embodiments, thecompounds described herein selectively inhibit a BET protein. In certainembodiments, the compounds described herein selectively inhibit BRD2. Incertain embodiments, the compounds described herein selectively inhibitBRD3. In certain embodiments, the compounds described herein selectivelyinhibit BRD4. In certain embodiments, the compounds described hereinselectively inhibit BRDT. In certain embodiments, the compoundsdescribed herein selectively inhibit a TAF protein (e.g., TAF1 orTAF1L), CBP, and/or EP300. In certain embodiments, a compound describedherein is a non-selective inhibitor of two or morebromodomain-containing proteins. In certain embodiments, a compounddescribed herein is a non-selective inhibitor of abromodomain-containing protein and a protein that is not abromodomain-containing protein.

The compounds described herein may also selectively bind to abromodomain of a bromodomain-containing protein. It is understood that,when a compound is referred to as “selectively” binding to a bromodomainof a bromodomain-containing protein, the compound binds to thebromodomain of the bromodomain-containing protein with a great affinitythan to a non-bromodomain of the bromodomain-containing protein.

The selectivity of a compound described herein in inhibiting theactivity of a bromodomain-containing protein over a second protein(e.g., a kinase) that is different from the bromodomain-containingprotein may be measured by the quotient of the IC₅₀ value of thecompound described herein in inhibiting the activity of the secondprotein over the IC₅₀ value of the compound described herein ininhibiting the activity of the bromodomain-containing protein. Theselectivity of a compound described herein for a bromodomain-containingprotein over second protein may also be measured by the quotient of theK_(d) value of an adduct of the compound described herein and the secondprotein over the K_(d) value of an adduct of the compound describedherein and the bromodomain-containing protein. In certain embodiments,the selectivity is at least about 1-fold, at least about 3-fold, atleast about 5-fold, at least about 10-fold, at least about 30-fold, atleast about 100-fold, at least about 300-fold, at least about1,000-fold, at least about 3,000-fold, at least about 10,000-fold, atleast about 30,000-fold, or at least about 100,000-fold. In certainembodiments, the selectivity is at most about 100,000-fold, at mostabout 10,000-fold, at most about 1,000-fold, at most about 100-fold, atmost about 10-fold, or at most about 1-fold. Combinations of theabove-referenced ranges (e.g., and at least about 2-fold and at mostabout 10,000-fold) are also within the scope of the invention. Otherranges are also possible. In certain embodiments, the selectivity is atleast about 3-fold. In certain embodiments, the selectivity is at leastabout 10-fold. In certain embodiments, the selectivity is at least about100-fold.

It is known in the art that a bromodomain-containing protein isimplicated in a wide range of diseases. For example, BRD3 and BRD4 arerelated to BRD3 NUT midline carcinoma and BRD4 NUT midline carcinoma,respectively, BRDT is related to sperm formation, and CBP is related tomixed-lineage leukemia (MLL). Therefore, the compounds described hereinare expected to be useful in treating and/or preventing diseasesassociated with bromodomain-containing proteins or as a malecontraceptive.

Pharmaceutical Compositions, Kits, and Administration

The present invention provides pharmaceutical compositions comprising acompound described herein (e.g., a compound of Formula (II) (e.g., acompound of Formula (I)), or a pharmaceutically acceptable salt,solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer,isotopically labeled derivative, or prodrug thereof), and optionally apharmaceutically acceptable excipient. In certain embodiments, thepharmaceutical composition described herein comprises a compound ofFormula (II), or a pharmaceutically acceptable salt thereof, andoptionally a pharmaceutically acceptable excipient. In certainembodiments, the pharmaceutical composition described herein comprises acompound of Formula (II), or a pharmaceutically acceptable salt thereof,and a pharmaceutically acceptable excipient.

In certain embodiments, the compound described herein is provided in aneffective amount in the pharmaceutical composition. In certainembodiments, the effective amount is a therapeutically effective amount.In certain embodiments, the effective amount is a prophylacticallyeffective amount. In certain embodiments, the effective amount is anamount effective for treating and/or preventing a disease (e.g., adisease described herein) in a subject in need thereof. In certainembodiments, the effective amount is an amount effective for treating adisease in a subject in need thereof. In certain embodiments, theeffective amount is an amount effective for preventing a disease in asubject in need thereof. In certain embodiments, the effective amount isan amount effective for reducing the risk of developing a disease in asubject in need thereof. In certain embodiments, the effective amount isan amount effective for contraception in a subject in need thereof. Incertain embodiments, the effective amount is an amount effective forinhibiting the replication of a virus. In certain embodiments, theeffective amount is an amount effective for kill a virus. In certainembodiments, the effective amount is an amount effective for inhibitingthe activity (e.g., aberrant activity, such as increased activity) of abromodomain-containing protein in a subject or cell. In certainembodiments, the effective amount is an amount effective for inhibitingthe activity (e.g., aberrant activity, such as increased activity) of abromodomain in a subject or cell. In certain embodiments, the effectiveamount is an amount effective for inhibiting the binding of abromodomain of a bromodomain-containing protein to an acetyl-lysineresidue of a second protein (e.g., a histone) in a subject or cell. Incertain embodiments, the effective amount is an amount effective formodulating (e.g., inhibiting) transcriptional elongation in a subject orcell. In certain embodiments, the effective amount is an amounteffective for modulating (e.g., down-regulating or inhibiting) theexpression (e.g., transcription) of a gene that is regulated by abromodomain-containing protein in a subject or cell. In certainembodiments, the effective amount is an amount effective for modulating(e.g., reducing) the level of a bromodomain-containing protein in asubject or cell.

An effective amount of a compound may vary from about 0.001 mg/kg toabout 1000 mg/kg in one or more dose administrations for one or severaldays (depending on the mode of administration). In certain embodiments,the effective amount per dose varies from about 0.001 mg/kg to about1000 mg/kg, from about 0.01 mg/kg to about 750 mg/kg, from about 0.1mg/kg to about 500 mg/kg, from about 1.0 mg/kg to about 250 mg/kg, andfrom about 10.0 mg/kg to about 150 mg/kg.

In certain embodiments, the effective amount is an amount effective forinhibiting the activity of a bromodomain-containing protein, theactivity of a bromodomain, the binding of a bromodomain of abromodomain-containing protein to an acetyl-lysine residue of a secondprotein (e.g., a histone), the transcriptional elongation, and/or theexpression (e.g., transcription) of a gene that is regulated by abromodomain-containing protein by at least about 10%, at least about20%, at least about 30%, at least about 40%, at least about 50%, atleast about 60%, at least about 70%, at least about 80%, or at leastabout 90%. In certain embodiments, the effective amount is an amounteffective for inhibiting the activity of a bromodomain-containingprotein, the binding of a bromodomain of a bromodomain-containingprotein to an acetyl-lysine residue of a second protein (e.g., ahistone), and/or the expression (e.g., transcription) of a gene that isregulated by a bromodomain-containing protein by at most about 90%, atmost about 80%, at most about 70%, at most about 60%, at most about 50%,at most about 40%, at most about 30%, at most about 20%, or at mostabout 10%. Combinations of the ranges described herein (e.g., at leastabout 20% and at most about 50%) are also within the scope of theinvention. In certain embodiments, the activity of abromodomain-containing protein, the binding of a bromodomain of abromodomain-containing protein to an acetyl-lysine residue of a secondprotein (e.g., a histone), and/or the expression (e.g., transcription)of a gene that is regulated by a bromodomain-containing protein areinhibited by a percentage or a range of percentage described herein byan effective amount of a compound described herein.

In certain embodiments, the gene regulated by a bromodomain-containingprotein is a gene regulated by a bromo and extra terminal protein (BET).In certain embodiments, the gene regulated by a bromodomain-containingprotein is BRD2. In certain embodiments, the gene regulated by abromodomain-containing protein is BRD2(1). In certain embodiments, thegene regulated by a bromodomain-containing protein is BRD2(2). Incertain embodiments, the gene regulated by a bromodomain-containingprotein is BRD3. In certain embodiments, the gene regulated by abromodomain-containing protein is BRD3(1). In certain embodiments, thegene regulated by a bromodomain-containing protein is BRD3(2). Incertain embodiments, the gene regulated by a bromodomain-containingprotein is BRD4. In certain embodiments, the gene regulated by abromodomain-containing protein is BRD4(1). In certain embodiments, thegene regulated by a bromodomain-containing protein is BRD4(2). Incertain embodiments, the gene regulated by a bromodomain-containingprotein is BRDT. In certain embodiments, the gene regulated by abromodomain-containing protein is BRDT(1). In certain embodiments, thegene regulated by a bromodomain-containing protein is BRDT(2). Incertain embodiments, the gene regulated by a bromodomain-containingprotein is a gene regulated by a TBP (TATA box bindingprotein)-associated factor protein (TAF). In certain embodiments, thegene regulated by a bromodomain-containing protein is TAF1. In certainembodiments, the gene regulated by a bromodomain-containing protein isTAF1L. In certain embodiments, the gene regulated by abromodomain-containing protein is a gene regulated by a CREB-bindingprotein (CBP). In certain embodiments, the gene regulated by abromodomain-containing protein is a gene regulated by an E1A bindingprotein p300 (EP300).

Pharmaceutical compositions described herein can be prepared by anymethod known in the art of pharmacology. In general, such preparatorymethods include the steps of bringing the compound described herein(i.e., the “active ingredient”) into association with a carrier orexcipient, and/or one or more other accessory ingredients, and then, ifnecessary and/or desirable, shaping, and/or packaging the product into adesired single- or multi-dose unit.

Pharmaceutical compositions can be prepared, packaged, and/or sold inbulk, as a single unit dose, and/or as a plurality of single unit doses.A “unit dose” is a discrete amount of the pharmaceutical compositioncomprising a predetermined amount of the active ingredient. The amountof the active ingredient is generally equal to the dosage of the activeingredient which would be administered to a subject and/or a convenientfraction of such a dosage such as, for example, one-half or one-third ofsuch a dosage.

Relative amounts of the active ingredient, the pharmaceuticallyacceptable excipient, and/or any additional ingredients in apharmaceutical composition described herein will vary, depending uponthe identity, size, and/or condition of the subject treated and furtherdepending upon the route by which the composition is to be administered.The composition may comprise between 0.1% and 100% (w/w) activeingredient.

Pharmaceutically acceptable excipients used in the manufacture ofprovided pharmaceutical compositions include inert diluents, dispersingand/or granulating agents, surface active agents and/or emulsifiers,disintegrating agents, binding agents, preservatives, buffering agents,lubricating agents, and/or oils. Excipients such as cocoa butter andsuppository waxes, coloring agents, coating agents, sweetening,flavoring, and perfuming agents may also be present in the composition.

Exemplary diluents include calcium carbonate, sodium carbonate, calciumphosphate, dicalcium phosphate, calcium sulfate, calcium hydrogenphosphate, sodium phosphate lactose, sucrose, cellulose,microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodiumchloride, dry starch, cornstarch, powdered sugar, and mixtures thereof.

Exemplary granulating and/or dispersing agents include potato starch,corn starch, tapioca starch, sodium starch glycolate, clays, alginicacid, guar gum, citrus pulp, agar, bentonite, cellulose, and woodproducts, natural sponge, cation-exchange resins, calcium carbonate,silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone)(crospovidone), sodium carboxymethyl starch (sodium starch glycolate),carboxymethyl cellulose, cross-linked sodium carboxymethyl cellulose(croscarmellose), methylcellulose, pregelatinized starch (starch 1500),microcrystalline starch, water insoluble starch, calcium carboxymethylcellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate,quaternary ammonium compounds, and mixtures thereof.

Exemplary surface active agents and/or emulsifiers include naturalemulsifiers (e.g., acacia, agar, alginic acid, sodium alginate,tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk,casein, wool fat, cholesterol, wax, and lecithin), colloidal clays(e.g., bentonite (aluminum silicate) and Veegum (magnesium aluminumsilicate)), long chain amino acid derivatives, high molecular weightalcohols (e.g., stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetinmonostearate, ethylene glycol distearate, glyceryl monostearate, andpropylene glycol monostearate, polyvinyl alcohol), carbomers (e.g.,carboxy polymethylene, polyacrylic acid, acrylic acid polymer, andcarboxyvinyl polymer), carrageenan, cellulosic derivatives (e.g.,carboxymethylcellulose sodium, powdered cellulose, hydroxymethylcellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose,methylcellulose), sorbitan fatty acid esters (e.g., polyoxyethylenesorbitan monolaurate (Tween® 20), polyoxyethylene sorbitan (Tween® 60),polyoxyethylene sorbitan monooleate (Tween® 80), sorbitan monopalmitate(Span® 40), sorbitan monostearate (Span® 60), sorbitan tristearate(Span® 65), glyceryl monooleate, sorbitan monooleate (Span® 80),polyoxyethylene esters (e.g., polyoxyethylene monostearate (Myrj® 45),polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil,polyoxymethylene stearate, and Solutol®), sucrose fatty acid esters,polyethylene glycol fatty acid esters (e.g., Cremophor®),polyoxyethylene ethers, (e.g., polyoxyethylene lauryl ether (Brij® 30)),poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamineoleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyllaurate, sodium lauryl sulfate, Pluronic® F-68, Poloxamer P-188,cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride,docusate sodium, and/or mixtures thereof.

Exemplary binding agents include starch (e.g., cornstarch and starchpaste), gelatin, sugars (e.g., sucrose, glucose, dextrose, dextrin,molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums(e.g., acacia, sodium alginate, extract of Irish moss, panwar gum,ghatti gum, mucilage of isapol husks, carboxymethylcellulose,methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl methylcellulose, microcrystalline cellulose,cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate(Veegum®), and larch arabogalactan), alginates, polyethylene oxide,polyethylene glycol, inorganic calcium salts, silicic acid,polymethacrylates, waxes, water, alcohol, and/or mixtures thereof.

Exemplary preservatives include antioxidants, chelating agents,antimicrobial preservatives, antifungal preservatives, antiprotozoanpreservatives, alcohol preservatives, acidic preservatives, and otherpreservatives. In certain embodiments, the preservative is anantioxidant. In other embodiments, the preservative is a chelatingagent.

Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbylpalmitate, butylated hydroxyanisole, butylated hydroxytoluene,monothioglycerol, potassium metabisulfite, propionic acid, propylgallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, andsodium sulfite.

Exemplary chelating agents include ethylenediaminetetraacetic acid(EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodiumedetate, trisodium edetate, calcium disodium edetate, dipotassiumedetate, and the like), citric acid and salts and hydrates thereof(e.g., citric acid monohydrate), fumaric acid and salts and hydratesthereof, malic acid and salts and hydrates thereof, phosphoric acid andsalts and hydrates thereof, and tartaric acid and salts and hydratesthereof. Exemplary antimicrobial preservatives include benzalkoniumchloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide,cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol,chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea,phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate,propylene glycol, and thimerosal.

Exemplary antifungal preservatives include butyl paraben, methylparaben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoicacid, potassium benzoate, potassium sorbate, sodium benzoate, sodiumpropionate, and sorbic acid.

Exemplary alcohol preservatives include ethanol, polyethylene glycol,phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate,and phenylethyl alcohol.

Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E,beta-carotene, citric acid, acetic acid, dehydroacetic acid, ascorbicacid, sorbic acid, and phytic acid.

Other preservatives include tocopherol, tocopherol acetate, deteroximemesylate, cetrimide, butylated hydroxyanisol (BHA), butylatedhydroxytoluened (BHT), ethylenediamine, sodium lauryl sulfate (SLS),sodium lauryl ether sulfate (SLES), sodium bisulfite, sodiummetabisulfite, potassium sulfite, potassium metabisulfite, Glydant®Plus, Phenonip®, methylparaben, Germall® 115, Germaben® II, Neolone®,Kathon®, and Euxyl®.

Exemplary buffering agents include citrate buffer solutions, acetatebuffer solutions, phosphate buffer solutions, ammonium chloride, calciumcarbonate, calcium chloride, calcium citrate, calcium glubionate,calcium gluceptate, calcium gluconate, D-gluconic acid, calciumglycerophosphate, calcium lactate, propanoic acid, calcium levulinate,pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasiccalcium phosphate, calcium hydroxide phosphate, potassium acetate,potassium chloride, potassium gluconate, potassium mixtures, dibasicpotassium phosphate, monobasic potassium phosphate, potassium phosphatemixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodiumcitrate, sodium lactate, dibasic sodium phosphate, monobasic sodiumphosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide,aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline,Ringer's solution, ethyl alcohol, and mixtures thereof.

Exemplary lubricating agents include magnesium stearate, calciumstearate, stearic acid, silica, talc, malt, glyceryl behanate,hydrogenated vegetable oils, polyethylene glycol, sodium benzoate,sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate,sodium lauryl sulfate, and mixtures thereof.

Exemplary natural oils include almond, apricot kernel, avocado, babassu,bergamot, black current seed, borage, cade, camomile, canola, caraway,carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee,corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed,geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate,jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademianut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange,orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed,pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood,sasquana, savoury, sea buckthorn, sesame, shea butter, silicone,soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, andwheat germ oils. Exemplary synthetic oils include, but are not limitedto, butyl stearate, caprylic triglyceride, capric triglyceride,cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate,mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and mixturesthereof.

Liquid dosage forms for oral and parenteral administration includepharmaceutically acceptable emulsions, microemulsions, solutions,suspensions, syrups and elixirs. In addition to the active ingredients,the liquid dosage forms may comprise inert diluents commonly used in theart such as, for example, water or other solvents, solubilizing agentsand emulsifiers such as ethyl alcohol, isopropyl alcohol, ethylcarbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed,groundnut, corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can include adjuvants such as wetting agents, emulsifyingand suspending agents, sweetening, flavoring, and perfuming agents. Incertain embodiments for parenteral administration, the conjugatesdescribed herein are mixed with solubilizing agents such as Cremophor®,alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins,polymers, and mixtures thereof.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions can be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation can be a sterile injectable solution,suspension, or emulsion in a nontoxic parenterally acceptable diluent orsolvent, for example, as a solution in 1,3-butanediol. Among theacceptable vehicles and solvents that can be employed are water,Ringer's solution, U.S.P., and isotonic sodium chloride solution. Inaddition, sterile, fixed oils are conventionally employed as a solventor suspending medium. For this purpose any bland fixed oil can beemployed including synthetic mono- or di-glycerides. In addition, fattyacids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, byfiltration through a bacterial-retaining filter, or by incorporatingsterilizing agents in the form of sterile solid compositions which canbe dissolved or dispersed in sterile water or other sterile injectablemedium prior to use.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This can be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolution,which, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform may be accomplished by dissolving or suspending the drug in an oilvehicle.

Compositions for rectal or vaginal administration are typicallysuppositories which can be prepared by mixing the conjugates describedherein with suitable non-irritating excipients or carriers such as cocoabutter, polyethylene glycol, or a suppository wax which are solid atambient temperature but liquid at body temperature and therefore melt inthe rectum or vaginal cavity and release the active ingredient.

Solid dosage forms for oral administration include capsules, tablets,pills, powders, and granules. In such solid dosage forms, the activeingredient is mixed with at least one inert, pharmaceutically acceptableexcipient or carrier such as sodium citrate or dicalcium phosphateand/or (a) fillers or extenders such as starches, lactose, sucrose,glucose, mannitol, and silicic acid, (b) binders such as, for example,carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone,sucrose, and acacia, (c) humectants such as glycerol, (d) disintegratingagents such as agar, calcium carbonate, potato or tapioca starch,alginic acid, certain silicates, and sodium carbonate, (e) solutionretarding agents such as paraffin, (f) absorption accelerators such asquaternary ammonium compounds, (g) wetting agents such as, for example,cetyl alcohol and glycerol monostearate, (h) absorbents such as kaolinand bentonite clay, and (i) lubricants such as talc, calcium stearate,magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate,and mixtures thereof. In the case of capsules, tablets, and pills, thedosage form may include a buffering agent.

Solid compositions of a similar type can be employed as fillers in softand hard-filled gelatin capsules using such excipients as lactose ormilk sugar as well as high molecular weight polyethylene glycols and thelike. The solid dosage forms of tablets, dragees, capsules, pills, andgranules can be prepared with coatings and shells such as entericcoatings and other coatings well known in the art of pharmacology. Theymay optionally comprise opacifying agents and can be of a compositionthat they release the active ingredient(s) only, or preferentially, in acertain part of the intestinal tract, optionally, in a delayed manner.Examples of encapsulating compositions which can be used includepolymeric substances and waxes. Solid compositions of a similar type canbe employed as fillers in soft and hard-filled gelatin capsules usingsuch excipients as lactose or milk sugar as well as high molecularweight polethylene glycols and the like.

The active ingredient can be in a micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings, and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active ingredient can be admixed with at least oneinert diluent such as sucrose, lactose, or starch. Such dosage forms maycomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may comprise bufferingagents. They may optionally comprise opacifying agents and can be of acomposition that they release the active ingredient(s) only, orpreferentially, in a certain part of the intestinal tract, optionally,in a delayed manner. Examples of encapsulating agents which can be usedinclude polymeric substances and waxes.

Dosage forms for topical and/or transdermal administration of a compounddescribed herein may include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants, and/or patches. Generally, theactive ingredient is admixed under sterile conditions with apharmaceutically acceptable carrier or excipient and/or any neededpreservatives and/or buffers as can be required. Additionally, thepresent invention contemplates the use of transdermal patches, whichoften have the added advantage of providing controlled delivery of anactive ingredient to the body. Such dosage forms can be prepared, forexample, by dissolving and/or dispensing the active ingredient in theproper medium. Alternatively or additionally, the rate can be controlledby either providing a rate controlling membrane and/or by dispersing theactive ingredient in a polymer matrix and/or gel.

Suitable devices for use in delivering intradermal pharmaceuticalcompositions described herein include short needle devices such as thosedescribed in U.S. Pat. Nos. 4,886,499; 5,190,521; 5,328,483; 5,527,288;4,270,537; 5,015,235; 5,141,496; and 5,417,662. Intradermal compositionscan be administered by devices which limit the effective penetrationlength of a needle into the skin, such as those described in PCTpublication WO 99/34850 and functional equivalents thereof.Alternatively or additionally, conventional syringes can be used in theclassical mantoux method of intradermal administration. Jet injectiondevices which deliver liquid vaccines to the dermis via a liquid jetinjector and/or via a needle which pierces the stratum corneum andproduces a jet which reaches the dermis are suitable. Jet injectiondevices are described, for example, in U.S. Pat. Nos. 5,480,381;5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911;5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627;5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460; andPCT publications WO 97/37705 and WO 97/13537. Ballistic powder/particledelivery devices which use compressed gas to accelerate the compound inpowder form through the outer layers of the skin to the dermis aresuitable.

Formulations suitable for topical administration include, but are notlimited to, liquid and/or semi-liquid preparations such as liniments,lotions, oil-in-water and/or water-in-oil emulsions such as creams,ointments, and/or pastes, and/or solutions and/or suspensions. Topicallyadministrable formulations may, for example, comprise from about 1% toabout 10% (w/w) active ingredient, although the concentration of theactive ingredient can be as high as the solubility limit of the activeingredient in the solvent. Formulations for topical administration mayfurther comprise one or more of the additional ingredients describedherein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation suitable for pulmonary administration viathe buccal cavity. Such a formulation may comprise dry particles whichcomprise the active ingredient and which have a diameter in the rangefrom about 0.5 to about 7 nanometers, or from about 1 to about 6nanometers. Such compositions are conveniently in the form of drypowders for administration using a device comprising a dry powderreservoir to which a stream of propellant can be directed to dispersethe powder and/or using a self-propelling solvent/powder dispensingcontainer such as a device comprising the active ingredient dissolvedand/or suspended in a low-boiling propellant in a sealed container. Suchpowders comprise particles wherein at least 98% of the particles byweight have a diameter greater than 0.5 nanometers and at least 95% ofthe particles by number have a diameter less than 7 nanometers.Alternatively, at least 95% of the particles by weight have a diametergreater than 1 nanometer and at least 90% of the particles by numberhave a diameter less than 6 nanometers. Dry powder compositions mayinclude a solid fine powder diluent such as sugar and are convenientlyprovided in a unit dose form.

Low boiling propellants generally include liquid propellants having aboiling point of below 65° F. at atmospheric pressure. Generally thepropellant may constitute 50 to 99.9% (w/w) of the composition, and theactive ingredient may constitute 0.1 to 20% (w/w) of the composition.The propellant may further comprise additional ingredients such as aliquid non-ionic and/or solid anionic surfactant and/or a solid diluent(which may have a particle size of the same order as particlescomprising the active ingredient).

Pharmaceutical compositions described herein formulated for pulmonarydelivery may provide the active ingredient in the form of droplets of asolution and/or suspension. Such formulations can be prepared, packaged,and/or sold as aqueous and/or dilute alcoholic solutions and/orsuspensions, optionally sterile, comprising the active ingredient, andmay conveniently be administered using any nebulization and/oratomization device. Such formulations may further comprise one or moreadditional ingredients including, but not limited to, a flavoring agentsuch as saccharin sodium, a volatile oil, a buffering agent, a surfaceactive agent, and/or a preservative such as methylhydroxybenzoate. Thedroplets provided by this route of administration may have an averagediameter in the range from about 0.1 to about 200 nanometers.

Formulations described herein as being useful for pulmonary delivery areuseful for intranasal delivery of a pharmaceutical composition describedherein. Another formulation suitable for intranasal administration is acoarse powder comprising the active ingredient and having an averageparticle from about 0.2 to 500 micrometers. Such a formulation isadministered by rapid inhalation through the nasal passage from acontainer of the powder held close to the nares.

Formulations for nasal administration may, for example, comprise fromabout as little as 0.1% (w/w) to as much as 100% (w/w) of the activeingredient, and may comprise one or more of the additional ingredientsdescribed herein. A pharmaceutical composition described herein can beprepared, packaged, and/or sold in a formulation for buccaladministration. Such formulations may, for example, be in the form oftablets and/or lozenges made using conventional methods, and maycontain, for example, 0.1 to 20% (w/w) active ingredient, the balancecomprising an orally dissolvable and/or degradable composition and,optionally, one or more of the additional ingredients described herein.Alternately, formulations for buccal administration may comprise apowder and/or an aerosolized and/or atomized solution and/or suspensioncomprising the active ingredient. Such powdered, aerosolized, and/oraerosolized formulations, when dispersed, may have an average particleand/or droplet size in the range from about 0.1 to about 200 nanometers,and may further comprise one or more of the additional ingredientsdescribed herein.

A pharmaceutical composition described herein can be prepared, packaged,and/or sold in a formulation for ophthalmic administration. Suchformulations may, for example, be in the form of eye drops including,for example, a 0.1-1.0% (w/w) solution and/or suspension of the activeingredient in an aqueous or oily liquid carrier or excipient. Such dropsmay further comprise buffering agents, salts, and/or one or more otherof the additional ingredients described herein. Otheropthalmically-administrable formulations which are useful include thosewhich comprise the active ingredient in microcrystalline form and/or ina liposomal preparation. Ear drops and/or eye drops are alsocontemplated as being within the scope of this invention.

Although the descriptions of pharmaceutical compositions provided hereinare principally directed to pharmaceutical compositions which aresuitable for administration to humans, it will be understood by theskilled artisan that such compositions are generally suitable foradministration to animals of all sorts. Modification of pharmaceuticalcompositions suitable for administration to humans in order to renderthe compositions suitable for administration to various animals is wellunderstood, and the ordinarily skilled veterinary pharmacologist candesign and/or perform such modification with ordinary experimentation.

Compounds provided herein are typically formulated in dosage unit formfor ease of administration and uniformity of dosage. It will beunderstood, however, that the total daily usage of the compositionsdescribed herein will be decided by the attending physician within thescope of sound medical judgment. The specific therapeutically effectivedose level for any particular subject or organism will depend upon avariety of factors including the disease being treated and the severityof the disorder; the activity of the specific active ingredientemployed; the specific composition employed; the age, body weight,general health, sex, and diet of the subject; the time ofadministration, route of administration, and rate of excretion of thespecific active ingredient employed; the duration of the treatment;drugs used in combination or coincidental with the specific activeingredient employed; and like factors well known in the medical arts.

The compounds and compositions provided herein can be administered byany route, including enteral (e.g., oral), parenteral, intravenous,intramuscular, intra-arterial, intramedullary, intrathecal,subcutaneous, intraventricular, transdermal, interdermal, rectal,intravaginal, intraperitoneal, topical (as by powders, ointments,creams, and/or drops), mucosal, nasal, bucal, sublingual; byintratracheal instillation, bronchial instillation, and/or inhalation;and/or as an oral spray, nasal spray, and/or aerosol. Specificallycontemplated routes are oral administration, intravenous administration(e.g., systemic intravenous injection), regional administration viablood and/or lymph supply, and/or direct administration to an affectedsite. In general, the most appropriate route of administration willdepend upon a variety of factors including the nature of the agent(e.g., its stability in the environment of the gastrointestinal tract),and/or the condition of the subject (e.g., whether the subject is ableto tolerate oral administration). In certain embodiments, the compoundor pharmaceutical composition described herein is suitable for topicaladministration to the eye of a subject.

The exact amount of a compound required to achieve an effective amountwill vary from subject to subject, depending, for example, on species,age, and general condition of a subject, severity of the side effects ordisorder, identity of the particular compound, mode of administration,and the like. The desired dosage can be delivered three times a day, twotimes a day, once a day, every other day, every third day, every week,every two weeks, every three weeks, or every four weeks. In certainembodiments, the desired dosage can be delivered using multipleadministrations (e.g., two, three, four, five, six, seven, eight, nine,ten, eleven, twelve, thirteen, fourteen, or more administrations). Aneffective amount may be included in a single dose (e.g., single oraldose) or multiple doses (e.g., multiple oral doses). In certainembodiments, when multiple doses are administered to a subject orapplied to a tissue or cell, any two doses of the multiple doses includedifferent or substantially the same amounts of a compound describedherein. In certain embodiments, when multiple doses are administered toa subject or applied to a tissue or cell, the frequency of administeringthe multiple doses to the subject or applying the multiple doses to thetissue or cell is three doses a day, two doses a day, one dose a day,one dose every other day, one dose every third day, one dose every week,one dose every two weeks, one dose every three weeks, or one dose everyfour weeks. In certain embodiments, the frequency of administering themultiple doses to the subject or applying the multiple doses to thetissue or cell is one dose per day. In certain embodiments, thefrequency of administering the multiple doses to the subject or applyingthe multiple doses to the tissue or cell is two doses per day. Incertain embodiments, the frequency of administering the multiple dosesto the subject or applying the multiple doses to the tissue or cell isthree doses per day. In certain embodiments, when multiple doses areadministered to a subject or applied to a tissue or cell, the durationbetween the first dose and last dose of the multiple doses is one day,two days, four days, one week, two weeks, three weeks, one month, twomonths, three months, four months, six months, nine months, one year,two years, three years, four years, five years, seven years, ten years,fifteen years, twenty years, or the lifetime of the subject, tissue, orcell. In certain embodiments, the duration between the first dose andlast dose of the multiple doses is three months, six months, or oneyear. In certain embodiments, the duration between the first dose andlast dose of the multiple doses is the lifetime of the subject, tissue,or cell. In certain embodiments, a dose (e.g., a single dose, or anydose of multiple doses) described herein includes independently between0.1 g and 1 g, between 0.001 mg and 0.01 mg, between 0.01 mg and 0.1 mg,between 0.1 mg and 1 mg, between 1 mg and 3 mg, between 3 mg and 10 mg,between 10 mg and 30 mg, between 30 mg and 100 mg, between 100 mg and300 mg, between 300 mg and 1,000 mg, or between 1 g and 10 g, inclusive,of a compound described herein. In certain embodiments, a dose describedherein includes independently between 1 mg and 3 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 3 mg and 10 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 10 mg and 30 mg, inclusive, of acompound described herein. In certain embodiments, a dose describedherein includes independently between 30 mg and 100 mg, inclusive, of acompound described herein.

In certain embodiments, an effective amount of a compound foradministration one or more times a day to a 70 kg adult human maycomprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg,about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about1000 mg, or about 100 mg to about 1000 mg, of a compound per unit dosageform.

In certain embodiments, the compounds described herein may be at dosagelevels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg,from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kgto about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg,from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, ofsubject body weight per day, one or more times a day, to obtain thedesired therapeutic and/or prophylactic effect.

It will be appreciated that dose ranges as described herein provideguidance for the administration of provided pharmaceutical compositionsto an adult. The amount to be administered to, for example, a child oran adolescent can be determined by a medical practitioner or personskilled in the art and can be lower or the same as that administered toan adult.

It will be also appreciated that a compound or composition, as describedherein, can be administered in combination with one or more additionalpharmaceutical agents (e.g., therapeutically and/or prophylacticallyactive agents). The compounds or compositions can be administered incombination with additional pharmaceutical agents that improve theiractivity (e.g., activity (e.g., potency and/or efficacy) in treating adisease in a subject in need thereof, in preventing a disease in asubject in need thereof, in reducing the risk to have a disease in asubject in need thereof, in inhibiting the replication of a virus, inkilling a virus, in inhibiting the activity of a bromodomain-containingprotein in a subject or cell, in inhibiting the activity of abromodomain in a subject or cell, in inhibiting the binding of abromodomain of a bromodomain-containing protein to an acetyl-lysineresidue of a second protein (e.g., a histone) in a subject or cell, inmodulating (e.g., inhibiting) the transcription elongation, inmodulating (e.g., inhibiting) the expression (e.g., transcription) of agene that is regulated by a bromodomain-containing protein in a subjector cell), in modulating (e.g., reducing) the level of abromodomain-containing protein in a subject or cell, bioavailability,and/or safety, reduce drug resistance, reduce and/or modify theirmetabolism, inhibit their excretion, and/or modify their distributionwithin the body of a subject. It will also be appreciated that thetherapy employed may achieve a desired effect for the same disorder,and/or it may achieve different effects. In certain embodiments, apharmaceutical composition described herein including a compounddescribed herein and an additional pharmaceutical agent shows asynergistic effect that is absent in a pharmaceutical compositionincluding one of the compound and the additional pharmaceutical agent,but not both.

The compound or composition can be administered concurrently with, priorto, or subsequent to one or more additional pharmaceutical agents, whichmay be useful as, e.g., combination therapies. Pharmaceutical agentsinclude therapeutically active agents. Pharmaceutical agents alsoinclude prophylactically active agents. Pharmaceutical agents includesmall organic molecules such as drug compounds (e.g., compounds approvedfor human or veterinary use by the U.S. Food and Drug Administration asprovided in the Code of Federal Regulations (CFR)), peptides, proteins,carbohydrates, monosaccharides, oligosaccharides, polysaccharides,nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides orproteins, small molecules linked to proteins, glycoproteins, steroids,nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides,antisense oligonucleotides, lipids, hormones, vitamins, and cells. Incertain embodiments, the additional pharmaceutical agent is apharmaceutical agent useful for treating and/or preventing a diseasedescribed herein. Each additional pharmaceutical agent may beadministered at a dose and/or on a time schedule determined for thatpharmaceutical agent. The additional pharmaceutical agents may also beadministered together with each other and/or with the compound orcomposition described herein in a single dose or administered separatelyin different doses. The particular combination to employ in a regimenwill take into account compatibility of the compound described hereinwith the additional pharmaceutical agent(s) and/or the desiredtherapeutic and/or prophylactic effect to be achieved. In general, it isexpected that the additional pharmaceutical agent(s) utilized incombination be utilized at levels that do not exceed the levels at whichthey are utilized individually. In some embodiments, the levels utilizedin combination will be lower than those utilized individually.

The additional pharmaceutical agents include, but are not limited to,anti-proliferative agents, anti-cancer agents, anti-angiogenesis agents,anti-inflammatory agents, immunosuppressants, anti-bacterial agents,anti-viral agents, cardiovascular agents, cholesterol-lowering agents,anti-diabetic agents, anti-allergic agents, contraceptive agents, andpain-relieving agents. In certain embodiments, the additionalpharmaceutical agent is an anti-proliferative agent. In certainembodiments, the additional pharmaceutical agent is an anti-canceragent. In certain embodiments, the additional pharmaceutical agent is ananti-leukemia agent. In certain embodiments, the additionalpharmaceutical agent is ABITREXATE (methotrexate), ADE, Adriamycin RDF(doxorubicin hydrochloride), Ambochlorin (chlorambucil), ARRANON(nelarabine), ARZERRA (ofatumumab), BOSULIF (bosutinib), BUSULFEX(busulfan), CAMPATH (alemtuzumab), CERUBIDINE (daunorubicinhydrochloride), CLAFEN (cyclophosphamide), CLOFAREX (clofarabine),CLOLAR (clofarabine), CVP, CYTOSAR-U (cytarabine), CYTOXAN(cyclophosphamide), ERWINAZE (Asparaginase Erwinia Chrysanthemi),FLUDARA (fludarabine phosphate), FOLEX (methotrexate), FOLEX PFS(methotrexate), GAZYVA (obinutuzumab), GLEEVEC (imatinib mesylate),Hyper-CVAD, ICLUSIG (ponatinib hydrochloride), IMBRUVICA (ibrutinib),LEUKERAN (chlorambucil), LINFOLIZIN (chlorambucil), MARQIBO (vincristinesulfate liposome), METHOTREXATE LPF (methorexate), MEXATE(methotrexate), MEXATE-AQ (methotrexate), mitoxantrone hydrochloride,MUSTARGEN (mechlorethamine hydrochloride), MYLERAN (busulfan), NEOSAR(cyclophosphamide), ONCASPAR (Pegaspargase), PURINETHOL(mercaptopurine), PURIXAN (mercaptopurine), Rubidomycin (daunorubicinhydrochloride), SPRYCEL (dasatinib), SYNRIBO (omacetaxinemepesuccinate), TARABINE PFS (cytarabine), TASIGNA (nilotinib), TREANDA(bendamustine hydrochloride), TRISENOX (arsenic trioxide), VINCASAR PFS(vincristine sulfate), ZYDELIG (idelalisib), or a combination thereof.In certain embodiments, the additional pharmaceutical agent is ananti-lymphoma agent. In certain embodiments, the additionalpharmaceutical agent is ABITREXATE (methotrexate), ABVD, ABVE, ABVE-PC,ADCETRIS (brentuximab vedotin), ADRIAMYCIN PFS (doxorubicinhydrochloride), ADRIAMYCIN RDF (doxorubicin hydrochloride), AMBOCHLORIN(chlorambucil), AMBOCLORIN (chlorambucil), ARRANON (nelarabine),BEACOPP, BECENUM (carmustine), BELEODAQ (belinostat), BEXXAR(tositumomab and iodine I 131 tositumomab), BICNU (carmustine),BLENOXANE (bleomycin), CARMUBRIS (carmustine), CHOP, CLAFEN(cyclophosphamide), COPP, COPP-ABV, CVP, CYTOXAN (cyclophosphamide),DEPOCYT (liposomal cytarabine), DTIC-DOME (dacarbazine), EPOCH, FOLEX(methotrexate), FOLEX PFS (methotrexate), FOLOTYN (pralatrexate),HYPER-CVAD, ICE, IMBRUVICA (ibrutinib), INTRON A (recombinant interferonalfa-2b), ISTODAX (romidepsin), LEUKERAN (chlorambucil), LINFOLIZIN(chlorambucil), Lomustine, MATULANE (procarbazine hydrochloride),METHOTREXATE LPF (methotrexate), MEXATE (methotrexate), MEXATE-AQ(methotrexate), MOPP, MOZOBIL (plerixafor), MUSTARGEN (mechlorethaminehydrochloride), NEOSAR (cyclophosphamide), OEPA, ONTAK (denileukindiftitox), OPPA, R-CHOP, REVLIMID (lenalidomide), RITUXAN (rituximab),STANFORD V, TREANDA (bendamustine hydrochloride), VAMP, VELBAN(vinblastine sulfate), VELCADE (bortezomib), VELSAR (vinblastinesulfate), VINCASAR PFS (vincristine sulfate), ZEVALIN (ibritumomabtiuxetan), ZOLINZA (vorinostat), ZYDELIG (idelalisib), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isREVLIMID (lenalidomide), DACOGEN (decitabine), VIDAZA (azacitidine),CYTOSAR-U (cytarabine), IDAMYCIN (idarubicin), CERUBIDINE(daunorubicin), LEUKERAN (chlorambucil), NEOSAR (cyclophosphamide),FLUDARA (fludarabine), LEUSTATIN (cladribine), or a combination thereof.In certain embodiments, the additional pharmaceutical agent isABITREXATE (methotrexate), ABRAXANE (paclitaxel albumin-stabilizednanoparticle formulation), AC, AC-T, ADE, ADRIAMYCIN PFS (doxorubicinhydrochloride), ADRUCIL (fluorouracil), AFINITOR (everolimus), AFINITORDISPERZ (everolimus), ALDARA (imiquimod), ALIMTA (pemetrexed disodium),AREDIA (pamidronate disodium), ARIMIDEX (anastrozole), AROMASIN(exemestane), AVASTIN (bevacizumab), BECENUM (carmustine), BEP, BICNU(carmustine), BLENOXANE (bleomycin), CAF, CAMPTOSAR (irinotecanhydrochloride), CAPOX, CAPRELSA (vandetanib), CARBOPLATIN-TAXOL,CARMUBRIS (carmustine), CASODEX (bicalutamide), CEENU (lomustine),CERUBIDINE (daunorubicin hydrochloride), CERVARIX (recombinant HPVbivalent vaccine), CLAFEN (cyclophosphamide), CMF, COMETRIQ(cabozantinib-s-malate), COSMEGEN (dactinomycin), CYFOS (ifosfamide),CYRAMZA (ramucirumab), CYTOSAR-U (cytarabine), CYTOXAN(cyclophosphamide), DACOGEN (decitabine), DEGARELIX, DOXIL (doxorubicinhydrochloride liposome), DOXORUBICIN HYDROCHLORIDE, DOX-SL (doxorubicinhydrochloride liposome), DTIC-DOME (dacarbazine), EFUDEX (fluorouracil),ELLENCE (epirubicin hydrochloride), ELOXATIN (oxaliplatin), ERBITUX(cetuximab), ERIVEDGE (vismodegib), ETOPOPHOS (etoposide phosphate),EVACET (doxorubicin hydrochloride liposome), FARESTON (toremifene),FASLODEX (fulvestrant), FEC, FEMARA (letrozole), FLUOROPLEX(fluorouracil), FOLEX (methotrexate), FOLEX PFS (methotrexate), FOLFIRI,FOLFIRI-BEVACIZUMAB, FOLFIRI-CETUXIMAB, FOLFIRINOX, FOLFOX, FU-LV,GARDASIL (recombinant human papillomavirus (HPV) quadrivalent vaccine),GEMCITABINE-CISPLATIN, GEMCITABINE-OXALIPLATIN, GEMZAR (gemcitabinehydrochloride), GILOTRIF (afatinib dimaleate), GLEEVEC (imatinibmesylate), GLIADEL (carmustine implant), GLIADEL WAFER (carmustineimplant), HERCEPTIN (trastuzumab), HYCAMTIN (topotecan hydrochloride),IFEX (ifosfamide), IFOSFAMIDUM (ifosfamide), INLYTA (axitinib), INTRON A(recombinant interferon alfa-2b), IRESSA (gefitinib), IXEMPRA(ixabepilone), JAKAFI (ruxolitinib phosphate), JEVTANA (cabazitaxel),KADCYLA (ado-trastuzumab emtansine), KEYTRUDA (pembrolizumab), KYPROLIS(carfilzomib), LIPODOX (doxorubicin hydrochloride liposome), LUPRON(leuprolide acetate), LUPRON DEPOT (leuprolide acetate), LUPRON DEPOT-3MONTH (leuprolide acetate), LUPRON DEPOT-4 MONTH (leuprolide acetate),LUPRON DEPOT-PED (leuprolide acetate), MEGACE (megestrol acetate),MEKINIST (trametinib), METHAZOLASTONE (temozolomide), METHOTREXATE LPF(methotrexate), MEXATE (methotrexate), MEXATE-AQ (methotrexate),MITOXANTRONE HYDROCHLORIDE, MITOZYTREX (mitomycin c), MOZOBIL(plerixafor), MUSTARGEN (mechlorethamine hydrochloride), MUTAMYCIN(mitomycin c), MYLOSAR (azacitidine), NAVELBINE (vinorelbine tartrate),NEOSAR (cyclophosphamide), NEXAVAR (sorafenib tosylate), NOLVADEX(tamoxifen citrate), NOVALDEX (tamoxifen citrate), OFF, PAD, PARAPLAT(carboplatin), PARAPLATIN (carboplatin), PEG-INTRON (peginterferonalfa-2b), PEMETREXED DISODIUM, PERJETA (pertuzumab), PLATINOL(cisplatin), PLATINOL-AQ (cisplatin), POMALYST (pomalidomide),prednisone, PROLEUKIN (aldesleukin), PROLIA (denosumab), PROVENGE(sipuleucel-t), REVLIMID (lenalidomide), RUBIDOMYCIN (daunorubicinhydrochloride), SPRYCEL (dasatinib), STIVARGA (regorafenib), SUTENT(sunitinib malate), SYLATRON (peginterferon alfa-2b), SYLVANT(siltuximab), SYNOVIR (thalidomide), TAC, TAFINLAR (dabrafenib),TARABINE PFS (cytarabine), TARCEVA (erlotinib hydrochloride), TASIGNA(nilotinib), TAXOL (paclitaxel), TAXOTERE (docetaxel), TEMODAR(temozolomide), THALOMID (thalidomide), TOPOSAR (etoposide), TORISEL(temsirolimus), TPF, TRISENOX (arsenic trioxide), TYKERB (lapatinibditosylate), VECTIBIX (panitumumab), VEIP, VELBAN (vinblastine sulfate),VELCADE (bortezomib), VELSAR (vinblastine sulfate), VEPESID (etoposide),VIADUR (leuprolide acetate), VIDAZA (azacitidine), VINCASAR PFS(vincristine sulfate), VOTRIENT (pazopanib hydrochloride), WELLCOVORIN(leucovorin calcium), XALKORI (crizotinib), XELODA (capecitabine),XELOX, XGEVA (denosumab), XOFIGO (radium 223 dichloride), XTANDI(enzalutamide), YERVOY (ipilimumab), ZALTRAP (ziv-aflibercept), ZELBORAF(vemurafenib), ZOLADEX (goserelin acetate), ZOMETA (zoledronic acid),ZYKADIA (ceritinib), ZYTIGA (abiraterone acetate), or a combinationthereof. In certain embodiments, the additional pharmaceutical agent isan anti-viral agent. In certain embodiments, the additionalpharmaceutical agent is a binder of a bromodomain-containing protein. Incertain embodiments, the additional pharmaceutical agent is a binder ofa bromodomain. In certain embodiments, the additional pharmaceuticalagent is a binder or inhibitor of a bromodomain-containing protein. Incertain embodiments, the additional pharmaceutical agent is an binder orinhibitor of a bromodomain. In certain embodiments, the additionalpharmaceutical agent is selected from the group consisting of epigeneticor transcriptional modulators (e.g., DNA methyltransferase inhibitors,histone deacetylase inhibitors (HDAC inhibitors), lysinemethyltransferase inhibitors), antimitotic drugs (e.g., taxanes andvinca alkaloids), hormone receptor modulators (e.g., estrogen receptormodulators and androgen receptor modulators), cell signaling pathwayinhibitors (e.g., tyrosine kinase inhibitors), modulators of proteinstability (e.g., proteasome inhibitors), Hsp90 inhibitors,glucocorticoids, all-trans retinoic acids, and other agents that promotedifferentiation. In certain embodiments, the compounds described hereinor pharmaceutical compositions can be administered in combination withan anti-cancer therapy including, but not limited to, surgery, radiationtherapy, transplantation (e.g., stem cell transplantation, bone marrowtransplantation), immunotherapy), and chemotherapy.

Also encompassed by the invention are kits (e.g., pharmaceutical packs).The kits provided may comprise a pharmaceutical composition or compounddescribed herein and a container (e.g., a vial, ampule, bottle, syringe,and/or dispenser package, or other suitable container). In someembodiments, provided kits may optionally further include a secondcontainer comprising a pharmaceutical excipient for dilution orsuspension of a pharmaceutical composition or compound described herein.In some embodiments, the pharmaceutical composition or compounddescribed herein provided in the first container and the secondcontainer are combined to form one unit dosage form.

Thus, in one aspect, provided are kits including a first containercomprising a compound described herein, or a pharmaceutically acceptablesalt, solvate, hydrate, polymorph, co-crystal, tautomer, stereoisomer,isotopically labeled derivative, or prodrug thereof, or a pharmaceuticalcomposition thereof. In certain embodiments, the kits are useful fortreating and/or preventing a disease described herein in a subject inneed thereof. In certain embodiments, the kits are useful for treating adisease described herein in a subject in need thereof. In certainembodiments, the kits are useful for preventing a disease describedherein in a subject in need thereof. In certain embodiments, the kitsare useful for reducing the risk of developing a disease describedherein in a subject in need thereof. In certain embodiments, the kitsare useful for contraception (e.g., male contraception). In certainembodiments, the kits are useful for in inhibiting the replication of avirus. In certain embodiments, the kits are useful for killing a virus.In certain embodiments, the kits are useful for inhibiting the activity(e.g., aberrant activity, such as increased activity) of abromodomain-containing protein in a subject or cell. In certainembodiments, the kits are useful for inhibiting the activity (e.g.,aberrant activity, such as increased activity) of a bromodomain in asubject or cell. In certain embodiments, the kits are useful forinhibiting the binding of a bromodomain of a bromodomain-containingprotein to an acetyl-lysine residue of a second protein (e.g., ahistone) in a subject or cell. In certain embodiments, the kits areuseful for modulating (e.g., inhibiting) the transcriptional elongationin a subject or cell. In certain embodiments, the kits are useful formodulating (e.g., down-regulating or inhibiting) the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein in a subject or cell. In certain embodiments, the kits areuseful for modulating (e.g., reducing) the level of abromodomain-containing protein in a subject or cell.

In certain embodiments, the kits are useful for screening a library ofcompounds to identify a compound that is useful in a method of theinvention.

In certain embodiments, a kit described herein further includesinstructions for using the kit, such as instructions for using the kitin a method of the invention (e.g., instructions for administering acompound or pharmaceutical composition described herein to a subject). Akit described herein may also include information as required by aregulatory agency such as the U.S. Food and Drug Administration (FDA).In certain embodiments, the information included in the kits isprescribing information. In certain embodiments, the kits andinstructions provide for treating and/or preventing a disease describedherein in a subject in need thereof. In certain embodiments, the kitsand instructions provide for treating a disease described herein in asubject in need thereof. In certain embodiments, the kits andinstructions provide for preventing a disease described herein in asubject in need thereof. In certain embodiments, the kits andinstructions provide for reducing the risk of developing a diseasedescribed herein in a subject in need thereof. In certain embodiments,the kits and instructions provide for contraception (e.g., malecontraception). In certain embodiments, the kits and instructionsprovide for inhibiting the replication of a virus. In certainembodiments, the kits and instructions provide for killing a virus. Incertain embodiments, the kits and instructions provide for inhibitingthe activity (e.g., aberrant activity, such as increased activity) of abromodomain-containing protein in a subject or cell. In certainembodiments, the kits and instructions provide for inhibiting theactivity (e.g., aberrant activity, such as increased activity) of abromodomain in a subject or cell. In certain embodiments, the kits andinstructions provide for inhibiting the binding of a bromodomain of abromodomain-containing protein to an acetyl-lysine residue of a secondprotein (e.g., a histone) in a subject or cell. In certain embodiments,the kits and instructions provide for modulating (e.g., inhibiting) thetranscriptional elongation. In certain embodiments, the kits andinstructions provide for modulating (e.g., down-regulating orinhibiting) the expression (e.g., transcription) of a gene that isregulated by a bromodomain-containing protein in a subject or cell. Incertain embodiments, the kits and instructions provide for modulating(e.g., reducing) the level of a bromodomain-containing protein in asubject or cell. In certain embodiments, the kits and instructionsprovide for screening a library of compounds to identify a compound thatis useful in a method of the invention. A kit described herein mayinclude one or more additional pharmaceutical agents described herein asa separate composition.

Methods of Treatment and Uses

The present invention provides methods for the treatment of a wide rangeof diseases, such as diseases associated with bromodomains, diseasesassociated with the activity (e.g., aberrant activity) of bromodomains,diseases associated with bromodomain-containing proteins, and diseaseassociated with the activity (e.g., aberrant activity) ofbromodomain-containing proteins. Exemplary diseases include, but are notlimited to, proliferative diseases, cardiovascular diseases, viralinfections, fibrotic diseases, metabolic diseases, endocrine diseases,and radiation poisoning. Also provided by the present invention aremethods for contraception (e.g., male contraception). The presentinvention further provides methods of inhibiting the activity (e.g.,aberrant activity, such as increased activity) of a bromodomain orbromodomain-containing protein, methods of inhibiting the binding of abromodomain of a bromodomain-containing protein to an acetyl-lysineresidue of a second protein (e.g., a histone), methods of modulating(e.g., inhibiting) the transcriptional elongation, and methods ofmodulating (e.g., down-regulating or inhibiting) the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein.

Gene regulation is fundamentally governed by reversible, non-covalentassembly of macromolecules. Signal transduction to RNA polymeraserequires higher-ordered protein complexes, spatially regulated byassembly factors capable of interpreting the post-translationalmodification states of chromatin. Epigenetic readers are structurallydiverse proteins, and each of the epigenetic readers possesses one ormore evolutionarily conserved effector modules, which recognize covalentmodifications of proteins (e.g., histones) or DNA. The ε-N-acetylationof lysine residues (Kac) on histone tails is associated with an openchromatin architecture and transcriptional activation. Context-specificmolecular recognition of acetyl-lysine is principally mediated bybromodomains.

Bromodomain-containing proteins are of substantial biological interest,as components of transcription factor complexes (e.g., TBP (TATA boxbinding protein)-associated factor 1 (TAF1), CREB-binding protein (CBPor CREBBP), P300/CBP-associated factor (PCAF), and Gcn5) anddeterminants of epigenetic memory. There are 41 human proteinscontaining a total of 57 diverse bromodomains. Despite large sequencevariations, all bromodomains share a conserved fold comprising aleft-handed bundle of four alpha helices (α_(Z), α_(A), α_(B), andα_(C)), linked by diverse loop regions (ZA and BC loops) that determinesubstrate specificity. Co-crystal structures with peptidic substratesshowed that the acetyl-lysine is recognized by a central hydrophobiccavity and is anchored by a hydrogen bond with an asparagine residuepresent in most bromodomains. The bromo and extra-terminal (BET) family(e.g., BRD2, BRD3, BRD4 and BRDT) shares a common domain architecturecomprising two N-terminal bromodomains that exhibit high level ofsequence conservation, and a more divergent C-terminal recruitmentdomain.

Recent research has established a compelling rationale for targetingBRD4 in cancer. BRD4 functions to facilitate cell cycle progression andknock-down in cultured cancer cell lines prompts G1 arrest. BRD4 is animportant mediator of transcriptional elongation, functioning to recruitthe positive transcription elongation factor complex (P-TEFb). Cyclindependent kinase-9, a core component of P-TEFb, is a validated target inchronic lymphocytic leukemia, and has recently been linked to c-Mycdependent transcription. Bromodomains present in BRD4 recruit P-TEFb tomitotic chromosomes resulting in increased expression of growthpromoting genes. BRD4 remains bound to transcriptional start sites ofgenes expressed during M/G1 but has not been found present at startsites that are expressed later in the cell cycle. Knockdown of BRD4 inproliferating cells has been shown to lead to G1 arrest and apoptosis bydecreasing expression levels of genes important for mitotic progressionand survival.

Importantly, BRD4 has recently been identified as a component of arecurrent t(15;19) chromosomal translocation in an aggressive form ofhuman squamous cell carcinoma. Such translocations express the tandemN-terminal bromodomains of BRD4 as an in-frame chimera with the nuclearprotein in testis (NUT) protein, genetically defining the NUT midlinecarcinoma (NMC). Functional studies in patient-derived NMC cell lineshave validated the essential role of the BRD4-NUT oncoprotein inmaintaining the characteristic proliferation advantage anddifferentiation block of this malignancy. Notably, RNA silencing ofBRD4-NUT gene expression arrests proliferation and prompts squamousdifferentiation with a marked increase in cytokeratin expression. Abromodomain may also down-regulates Myc and other transcriptionalfactors, such as interleukin 7 receptor (IL7R). These observationsunderscore the utility and therapeutic potential of an binder orinhibitor of bromodomain-containing proteins.

In another aspect, the present invention provides methods of inhibitingthe activity of a bromodomain-containing protein in a subject or cell.In certain embodiments, the bromodomain-containing protein is abromodomain-containing protein described herein (e.g., a BET protein,such as BRD2, BRD3, BRD4, or BRDT). In certain embodiments, the activityof a bromodomain-containing protein in a subject or cell is inhibited bythe inventive methods. In certain embodiments, the activity of abromodomain-containing protein in a subject or cell is inhibited by theinventive methods by at least about 1%, at least about 3%, at leastabout 10%, at least about 20%, at least about 30%, at least about 40%,at least about 50%, at least about 60%, at least about 70%, at leastabout 80%, or at least about 90%. In certain embodiments, the activityof a bromodomain-containing protein in a subject or cell is inhibited bythe inventive methods by at most about 90%, at most about 80%, at mostabout 70%, at most about 60%, at most about 50%, at most about 40%, atmost about 30%, at most about 20%, at most about 10%, at most about 3%,or at most about 1%. Combinations of the above-referenced ranges (e.g.,at least about 10% and at most about 50%) are also within the scope ofthe invention. Other ranges are also possible. In some embodiments, theactivity of a bromodomain-containing protein in a subject or cell isselectively inhibited by the inventive methods. In some embodiments, theactivity of a bromodomain-containing protein in a subject or cell isselectively inhibited by the inventive methods, compared to the activityof a kinase (e.g., a MAP kinase, a mitotic spindle kinase, a polokinase). In other embodiments, the activity of a bromodomain-containingprotein in a subject or cell is non-selectively inhibited by theinventive methods. In certain embodiments, the cytokine level and/orhistamine release are reduced by the inventive methods.

In certain embodiments, the activity of a bromodomain-containing proteinis an aberrant activity of the bromodomain-containing protein. Incertain embodiments, the activity of a bromodomain-containing protein isan increased activity of the bromodomain-containing protein. In certainembodiments, the activity of a bromodomain-containing protein is reducedby a method of the invention.

In certain embodiments, the subject is an animal. The animal may be ofeither sex and may be at any stage of development. In certainembodiments, the subject is a male. In certain embodiments, the subjectis a female. In certain embodiments, the subject described herein is ahuman. In certain embodiments, the subject described herein is a humanmale. In certain embodiments, the subject described herein is a humanfemale. In certain embodiments, the subject is a human diagnosed ashaving a disease described herein. In certain embodiments, the subjectis a human diagnosed as being at a higher-than-normal risk to have adisease described herein. In certain embodiments, the subject is a humansuspected of having a disease described herein. In certain embodiments,the subject is a non-human animal. In certain embodiments, the subjectis a fish. In certain embodiments, the subject is a mammal. In certainembodiments, the subject is a non-human mammal. In certain embodiments,the subject is a human or non-human mammal. In certain embodiments, thesubject is a domesticated animal, such as a dog, cat, cow, pig, horse,sheep, or goat. In certain embodiments, the subject is a companionanimal such as a dog or cat. In certain embodiments, the subject is alivestock animal such as a cow, pig, horse, sheep, or goat. In certainembodiments, the subject is a zoo animal. In another embodiment, thesubject is a research animal such as a rodent (e.g., mouse, rat), dog,pig, or non-human primate. In certain embodiments, the animal is agenetically engineered animal. In certain embodiments, the animal is atransgenic animal (e.g., transgenic mice and transgenic pigs).

In certain embodiments, the cell described herein is present in vitro.In certain embodiments, the cell is present ex vivo. In certainembodiments, the cell is present in vivo.

In another aspect, the present invention provides methods of inhibitingthe activity of a bromodomain in a subject or cell. In certainembodiments, the activity of a bromodomain is an aberrant activity ofthe bromodomain. In certain embodiments, the activity of a bromodomainis an increased activity of the bromodomain. In certain embodiments, theactivity of a bromodomain is reduced by a method of the invention.

Another aspect of the present invention relates to methods of inhibitingthe binding of a bromodomain of a bromodomain-containing protein to anacetyl-lysine residue of a second protein (e.g., a histone) in a subjector cell. In certain embodiments, the second protein is a proteinincluding at least one acetyl-lysine residue. In certain embodiments,the second protein is not a bromodomain-containing protein. In certainembodiments, the second protein is a histone. In certain embodiments,the histone is selected from the group consisting of H1, H2A, H2B, H3,H4, and H5. In certain embodiments, the binding of a bromodomain of thebromodomain-containing protein to an acetyl-lysine residue of the secondprotein (e.g., a histone) is inhibited by the inventive methods.

In another aspect, the present invention provides methods of modulating(e.g., inhibiting) the transcription elongation. In certain embodiments,the transcription elongation is modulated (e.g., inhibited) by theinventive methods.

In another aspect, the present invention provides methods of modulatingthe expression (e.g., transcription) of a gene (e.g., a gene describedherein) that is regulated by a bromodomain-containing protein in asubject or cell. In certain embodiments, the present invention providesmethods of down-regulating or inhibiting the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein in a subject or cell. Without wishing to be bound by anyparticular theory, the compounds and pharmaceutical compositionsdescribed herein may be able to interfere with the binding of abromodomain-containing protein to a transcriptional start site of thegene. In certain embodiments, the compounds and pharmaceuticalcompositions described herein interfere with the acetyl-lysinerecognition during the expression (e.g., transcription) of the gene. Incertain embodiments, the compounds and pharmaceutical compositionsdescribed herein interfere with the acetyl-lysine anchoring during theexpression (e.g., transcription) of the gene. In certain embodiments,the expression (e.g., transcription) of a gene that is regulated by abromodomain-containing protein in a subject or cell is modulated by theinventive methods. In certain embodiments, the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein in a subject or cell is down-regulated or inhibited by theinventive methods. In certain embodiments, the gene that is regulated bya bromodomain-containing protein is an oncogene.

Another aspect of the present invention relates to methods of treating adisease in a subject in need thereof. In certain embodiments, thedisease is treated by the inventive methods.

In certain embodiments, the disease is a disease associated with abromodomain-containing protein. In certain embodiments, the disease is adisease associated with the activity of a bromodomain-containingprotein. In certain embodiments, the disease is a disease associatedwith the aberrant activity (e.g., increased activity) of abromodomain-containing protein.

In certain embodiments, the disease is a disease associated with abromodomain (e.g., a bromodomain of a bromodomain-containing protein).In certain embodiments, the disease is a disease associated with theactivity of a bromodomain. In certain embodiments, the disease is adisease associated with the aberrant activity (e.g., increased activity)of a bromodomain. In certain embodiments, the disease is a diseaseassociated with the function (e.g., dysfunction) of a bromodomain.

In certain embodiments, the disease described herein is driven by atranscriptional activator. In certain embodiments, the transcriptionalactivator is Myc. In certain embodiments, the disease is associated witha NUT rearrangement. In certain embodiments, the disease is a diseaseassociated with aberrant Myc function. In certain embodiments, thedisease is a disease associated with interleukin 7 receptor (IL7R).

In certain embodiments, the disease is a proliferative disease (e.g., aproliferative disease described herein). In certain embodiments, thedisease is cancer (e.g., a cancer described herein). In certainembodiments, the disease is lung cancer. In certain embodiments, thedisease is multiple myeloma. In certain embodiments, the disease isneuroblastoma. In certain embodiments, the disease is colon cancer. Incertain embodiments, the disease is testicular cancer. In certainembodiments, the disease is ovarian cancer. In certain embodiments, thedisease is lung cancer (e.g., small-cell lung cancer or non-small-celllung cancer). In certain embodiments, the disease is NUT midlinecarcinoma (e.g., BRD3 NUT midline carcinoma or BRD4 NUT midlinecarcinoma). In certain embodiments, the disease is leukemia. In certainembodiments, the disease is mixed-lineage leukemia (MLL). In certainembodiments, the disease is acute myelocytic leukemia (AML),biphenotypic B myelomonocytic leukemia, or erythroleukemia. In certainembodiments, the disease is selected from the group consisting ofBurkitt's lymphoma, breast cancer, colon cancer, neuroblastoma, glialblastoma multiforme, chronic lymphocytic leukemia, and squamous cellcarcinoma.

In certain embodiments, the disease is a benign neoplasm (e.g., a benignneoplasm described herein).

In certain embodiments, the disease is an inflammatory disease (e.g., aninflammatory disease described herein). In certain embodiments, thedisease is a disease that involves an inflammatory response to aninfection with a bacterium, virus, fungus, parasite, and/or protozoon.In certain embodiments, the disease is selected from the groupconsisting of osteoarthritis, acute gout, multiple sclerosis, aninflammatory bowel disease (e.g., Crohn's disease and ulcerativecolitis), neuroinflammation, asthma, a chronic obstructive airwaysdisease, pneumonitis, myositis, eczema, dermatitis, acne, cellulitis, anocclusive disease, thrombosis, alopecia, nephritis, vasculitis,retinitis, uveitis, scleritis, sclerosing cholangitis, hypophysitis,thyroiditis, septic shock, systemic inflammatory response syndrome(SIRS), toxic shock syndrome, acute lung injury, ARDS (adult respiratorydistress syndrome), acute renal failure, burns, pancreatitis (e.g.,acute pancreatitis), post-surgical syndromes, sarcoidosis, Herxheimerreactions, encephalitis, myelitis, meningitis, and malaria. In certainembodiments, the disease is acute or chronic pancreatitis. In certainembodiments, the disease is burns. In certain embodiments, the diseaseis an inflammatory bowel disease. In certain embodiments, the disease isneuroinflammation. In certain embodiments, the disease is sepsis orsepsis syndrome. In certain embodiments, the disease isgraft-versus-host disease (GVHD).

In certain embodiments, the disease is an autoimmune disease (e.g., anautoimmune disease described herein). In certain embodiments, thedisease is rheumatoid arthritis. In certain embodiments, the disease ispsoriasis, systemic lupus erythematosus, vitiligo, a bullous skindisease.

In certain embodiments, the disease is a cardiovascular disease. Incertain embodiments, the disease is atherogenesis or atherosclerosis. Incertain embodiments, the disease is arterial stent occlusion, heartfailure (e.g., congestive heart failure), a coronary arterial disease,myocarditis, pericarditis, a cardiac valvular disease, stenosis,restenosis, in-stent-stenosis, angina pectoris, myocardial infarction,acute coronary syndromes, coronary artery bypass grafting, acardio-pulmonary bypass procedure, endotoxemia, ischemia-reperfusioninjury, cerebrovascular ischemia (stroke), renal reperfusion injury,embolism (e.g., pulmonary, renal, hepatic, gastro-intestinal, orperipheral limb embolism), or myocardial ischemia.

In certain embodiments, the disease is a viral infection. In certainembodiments, the disease is a DNA virus infection. In certainembodiments, the disease is a dsDNA virus infection. In certainembodiments, the disease is an ssDNA virus infection. In certainembodiments, the disease is an RNA virus infection. In certainembodiments, the disease is a dsRNA virus infection. In certainembodiments, the disease is a (+)ssRNA virus infection. In certainembodiments, the disease is a (−)ssRNA virus infection. In certainembodiments, the disease is a reverse transcribing (RT) virus infection.In certain embodiments, the disease is an ssRNA-RT virus infection. Incertain embodiments, the disease is a dsDNA-RT virus infection. Incertain embodiments, the disease is human immunodeficiency virus (HIV)infection. In certain embodiments, the disease is acquiredimmunodeficiency syndrome (AIDS). In certain embodiments, the disease ishuman papillomavirus (HPV) infection. In certain embodiments, thedisease is hepatitis C virus (HCV) infection. In certain embodiments,the disease is a herpes virus infection (e.g., herpes simplex virus(HSV) infection). In certain embodiments, the disease is Ebola virusinfection. In certain embodiments, the disease is severe acuterespiratory syndrome (SARS). In certain embodiments, the disease isinfluenza virus infection. In certain embodiments, the disease is aninfluenza virus infection. In certain embodiments, the disease is aninfluenza A virus infection. In certain embodiments, the disease ishuman flu (e.g., H1N1, H2N2, H3N2, H5N1, H7N7, H1N2, H9N2, H7N2, H7N3,or H10N7 virus infection). In certain embodiments, the disease is birdflu (e.g., H5N1 or H7N9 virus infection). In certain embodiments, thedisease is swine influenza (e.g., H1N1, H1N2, H2N1, H3N1, H3N2, or H2N3virus infection, or influenza C virus infection). In certainembodiments, the disease is equine influenza (e.g., H7N7 or H3N8 virusinfection). In certain embodiments, the disease is canine influenza(e.g., H3N8 virus infection). In certain embodiments, the disease is aninfluenza B virus infection. In certain embodiments, the disease is aninfluenza C virus infection. In certain embodiments, the disease isDengue fever, Dengue hemorrhagic fever (DHF), Dengue shock syndrome(DSS), hepatitis A, hepatitis B, hepatitis D, hepatitis E, hepatitis F,Coxsackie A virus infection, Coxsackie B virus infection, fulminantviral hepatitis, viral myocarditis, parainfluenza virus infection, an RSvirus (RSV) infection (e.g., RSV bronchiolitis, RSV pneumonia,especially an infant and childhood RSV infection and RSV pneumonia inthe patients with cardiopulmonary disorders), measles virus infection,vesicular stomatitis virus infection, rabies virus infection, Japaneseencephalitis, Junin virus infection, human cytomegalovirus infection,varicellovirus infection, cytomegalovirus infection, muromegalovirusinfection, proboscivirus infection, roseolovirus infection,lymphocryptovirus infection, macavirus infection, percavirus infection,rhadinovirus infection), poliovirus infection, Marburg virus infection,Lassa fever virus infection, Venezuelan equine encephalitis, Rift ValleyFever virus infection, Korean hemorrhagic fever virus infection,Crimean-Congo hemorrhagic fever virus infection, encephalitis, SaintLouise encephalitis, Kyasanur Forest disease, Murray Valleyencephalitis, tick-borne encephalitis, West Nile encephalitis, yellowfever, adenovirus infection, poxvirus infection, or a viral infection insubjects with immune disorders.

In certain embodiments, the disease is a fibrotic condition. In certainembodiments, the disease is selected from the group consisting of renalfibrosis, post-operative stricture, keloid formation, hepatic cirrhosis,biliary cirrhosis, and cardiac fibrosis. In certain embodiments, thedisease is scleroderma. In certain embodiments, the disease isidiopathic pulmonary fibrosis.

In certain embodiments, the disease is an endocrine disease. In certainembodiments, the disease is Addison's disease.

In certain embodiments, the disease is a metabolic disease. In certainembodiments, the disease is diabetes. In certain embodiments, thedisease is type 1 diabetes. In certain embodiments, the disease is type2 diabetes or gestational diabetes. In certain embodiments, the diseaseis obesity. In certain embodiments, the disease is fatty liver (NASH orotherwise), cachexia, hypercholesterolemia, or a disorder of lipidmetabolism via the regulation of apolipoprotein A1 (APOA1).

In certain embodiments, the disease is radiation poisoning. In certainembodiments, the disease is radiation injury.

In certain embodiments, the disease is acute rejection of transplantedorgans or multi-organ dysfunction syndrome.

In certain embodiments, the disease is Alzheimer's disease.

In still another aspect, the present invention provides methods ofpreventing a disease described herein in a subject in need thereof. Incertain embodiments, the disease is prevented by the inventive methods.

In yet another aspect, the present invention provides methods ofreducing the risk to have a disease described herein in a subject inneed thereof. In certain embodiments, the risk to have the disease isreduced by the inventive methods.

In yet another aspect, the present invention provides methods forcontraception in a subject in need thereof. In certain embodiments, thepresent invention provides methods of male contraception in a malesubject in need thereof. In certain embodiments, the present inventionprovides methods of female contraception in a female subject in needthereof.

In yet another aspect, the present invention provides methods ofinhibiting sperm formation in a subject in need thereof.

Another aspect of the present invention relates to methods of inhibitingthe replication of a virus. In certain embodiments, the replication ofthe virus is inhibited by the inventive methods.

In certain embodiments, the virus is a virus described herein. Incertain embodiments, the virus is the virus causing a viral infectiondescribed herein. In certain embodiments, the virus is humanimmunodeficiency virus (HIV), human papillomavirus (HPV), hepatitis Cvirus (HCV), herpes simplex virus (HSV), Ebola virus, or influenzavirus.

In certain embodiments, the virus described herein is present in vitro.In certain embodiments, the virus is present ex vivo. In certainembodiments, the virus is present in vivo.

Another aspect of the present invention relates to methods of killing avirus. In certain embodiments, the virus is killed by the inventivemethods.

Another aspect of the invention relates to methods of inhibiting theinteraction between a bromodomain-containing protein and animmunoglobulin (Ig) regulatory element in a subject or cell.

In certain embodiments, the methods of the invention includeadministering to a subject in need thereof an effective amount of acompound or pharmaceutical composition described herein. In certainembodiments, the methods of the invention include administering to asubject in need thereof a therapeutically effective amount of a compoundor pharmaceutical composition described herein. In certain embodiments,the methods of the invention include administering to a subject in needthereof a prophylactically effective amount of a compound orpharmaceutical composition described herein. In certain embodiments, themethods of the invention include contacting a cell with an effectiveamount of a compound or pharmaceutical composition described herein. Incertain embodiments, the methods of the invention include contacting avirus with an effective amount of a compound or pharmaceuticalcomposition described herein.

Another aspect of the invention relates to methods of modulating genethat is regulated by a bromodomain-containing protein expressing in asubject or cell.

Another aspect of the invention relates to methods of modulating thelevel of a bromodomain-containing protein in a subject or cell.

Another aspect of the invention relates to methods of screening alibrary of compounds, and pharmaceutical acceptable salts thereof, toidentify a compound, or a pharmaceutical acceptable salt thereof, thatis useful in the methods of the invention. In certain embodiments, themethods of screening a library include obtaining at least two differentcompounds described herein; and performing at least one assay using thedifferent compounds described herein. In certain embodiments, at leastone assay is useful in identifying a compound that is useful in theinventive methods.

Typically, the methods of screening a library of compounds involve atleast one assay. In certain embodiments, the assay is performed todetect one or more characteristics associated with the treatment and/orprevention of a disease described herein, with the inhibition of theactivity of a bromodomain-containing protein, with the inhibition of theactivity of a bromodomain, with the inhibition of the binding of abromodomain to an acetyl-lysine residue of a second protein (e.g., ahistone), with the modulation (e.g., inhibition) of the transcriptionalelongation, and/or with the modulation (e.g., inhibition) of theexpression (e.g., transcription) of a gene that is regulated by abromodomain-containing protein. The characteristics may be desiredcharacteristics (e.g., a disease having been treated, a disease havingbeen prevented, the risk to have a disease having been reduced, thereplication of a virus having been inhibited, a virus having beenkilled, the activity of a bromodomain-containing protein having beeninhibited, the activity of a bromodomain, the binding of a bromodomainto an acetyl-lysine residue of a second protein (e.g., a histone) havingbeen inhibited, the transcriptional elongation having been modulated(e.g., having been inhibited), the level of a bromodomain-containingprotein in a subject or cell having been modulated (e.g., reduced), orthe expression (e.g., transcription) of a gene that is regulated by abromodomain-containing protein having been modulated (e.g., having beeninhibited)). The characteristics may be undesired characteristics (e.g.,a disease having not been treated, a disease having not been prevented,the risk to have a disease having not been reduced, the replication of avirus having not been inhibited, a virus not having been killed, theactivity of a bromodomain-containing protein having not been inhibited,the activity of a bromodomain having not been inhibited, the binding ofa bromodomain to an acetyl-lysine residue of a second protein (e.g., ahistone) having not been inhibited, the transcriptional elongationhaving not been modulated (e.g., having not been inhibited), the levelof a bromodomain-containing protein in a subject or cell having not beenmodulated (e.g., having not been reduced), or the expression (e.g.,transcription) of a gene that is regulated by a bromodomain-containingprotein having not been modulated (e.g., having not been inhibited)).The assay may be an immunoassay, such as a sandwich-type assay,competitive binding assay, one-step direct test, two-step test, or blotassay. The step of performing at least one assay may be performedrobotically or manually. In certain embodiments, the assay comprises (a)contacting a library of compounds with a bromodomain-containing protein;and (b) detecting the binding of the library of compounds to thebromodomain-containing protein. In certain embodiments, the assaycomprises detecting the specific binding of the library of compounds tothe bromodomain-containing protein. In certain embodiments, the assaycomprises detecting the specific binding of the library of compounds toa bromodomain of the bromodomain-containing protein. In certainembodiments, the detected binding of the library of compounds to thebromodomain-containing protein is useful in identifying the compoundthat is useful in the methods of the invention. In certain embodiments,the step of detecting the binding comprises using differential scanningfluorimetry (DSF), isothermal titration calorimetry (ITC), and/or anamplified luminescence proximity homogeneous assay (ALPHA). The step ofperforming at least one assay may be performed in a cell (e.g., a cancercell) in vitro, ex vivo, or in vivo. In certain embodiments, the step ofperforming at least one assay is performed in a cell (e.g., a cancercell) in vitro. In certain embodiments, the assay comprises (a)contacting a library of compounds with a cell; and (b) detecting adecrease in cell proliferation, an increase in cell death, and/or anincrease in cell differentiation. In certain embodiments, the cell deathis apoptotic cell death. In certain embodiments, the celldifferentiation is identified by detecting an increase in cytokeratinexpression. In certain embodiments, the step of performing at least oneassay further comprises detecting a reduction in transcriptionalelongation.

In another aspect, the present invention provides the compoundsdescribed herein for use in a method of the invention.

In still another aspect, the present invention provides thepharmaceutical compositions described herein for use in a method of theinvention.

In still another aspect, the present invention provides uses of thecompounds described herein in a method of the invention.

In further another aspect, the present invention provides uses of thepharmaceutical compositions described herein in a method of theinvention.

EXAMPLES

In order that the invention described herein may be more fullyunderstood, the following examples are set forth. The synthetic andbiological examples described in this application are offered toillustrate the compounds, pharmaceutical compositions, and methodsprovided herein and are not to be construed in any way as limiting theirscope.

Preparation of Compounds

The compounds provided herein can be prepared from readily availablestarting materials using the following general methods and procedures ormethods known in the art (e.g., methods reported in U.S. PatentApplication Publication, US 2012/040961; Elkins et al., Journal ofMedicinal Chemistry (2013), 56(11), 4413-4421; Kavanagh et al.,Bioorganic & Medicinal Chemistry Letters (2013), 23(13), 3690-3696; Denget al., European Journal of Medicinal Chemistry (2013), 70, 758-767;Delbroek et al., Journal of Pharmaceutical and Biomedical Analysis(2013), 76, 49-58; Choi et al., ACS Medicinal Chemistry Letters (2012),3(8), 658-662; Deng et al., Nature Chemical Biology (2011), 7(4),203-205; and Deng et al., ACS Medicinal Chemistry Letters (2011), 2(3),195-200). It will be appreciated that where typical or preferred processconditions (i.e., reaction temperatures, times, mole ratios ofreactants, solvents, pressures, etc.) are given, other processconditions can also be used unless otherwise stated. Optimum reactionconditions may vary with the particular reactants or solvents used, butsuch conditions can be determined by those skilled in the art by routineoptimization procedures.

Various established synthetic methods may be used to arrive at theinventive compounds described herein. In one embodiment, the inventivecompounds can be prepared using the sequence provided in Scheme 1. Amineaddition of S-1 into nitropyrimidines S-2 wherein X² and X³ are eachindependently halide (e.g. fluoro, chloro, bromo, or iodo) provideintermediates S-3 wherein R^(E1) is hydrogen or substituted orunsubstituted alkyl. In some embodiments, both X² and X³ are chloro.Reduction of the nitro functionality in S-3 produces compounds S-4. Incertain embodiments, the reduction conditions comprise a metal catalyst;e.g. palladium on carbon or Raney nickel. In certain embodiments, thereduction conditions comprise a metal at the (0) oxidation state; e.g.iron(0), tin(0), zinc(0). In certain embodiments, the reductionconditions comprise addition of an acid; e.g. acetic or hydrochloricacid. Cyclization of the free amino group leads to compounds S-5. Incertain embodiments, the reduction and cyclization steps occur inone-pot. In certain embodiments, the cyclization conditions comprise anamide coupling agent; e.g. HATU or EDC. Various leaving group conjugatesof R^(E) (i.e. LG-R^(E), wherein LG is a leaving group as definedherein) can be contacted with compounds S-5 under appropriate conditionsto afford intermediates S-6. In certain embodiments, the conditionscomprise a base. In some embodiments, the conditions comprise aninorganic base; e.g. sodium hydride. In certain embodiments, the leavinggroup conjugate of R³ is a halide; e.g. bromo or iodo. Subsequentlinkage to the sidechain S-7 can be accomplished under aromaticsubstitution or coupling conditions to product compounds of Formula (I).In certain embodiments, the conditions comprise a base. In someembodiments, the conditions comprise an inorganic base; e.g. potassiumor sodium carbonate. In certain embodiments, the conditions comprise atransition metal catalyst; e.g. a palladium or nickel catalyst. Incertain embodiments, the conditions comprise a ligand; e.g. a phosphineligand such as X-phos. In certain embodiments, compounds of S-6 can bealternatively modified by leaving group conjugates of R^(F) (i.e.LG-R^(F), wherein LG is a leaving group as defined herein) followingcyclization. In certain embodiments, precursors to compounds of Formula(I) can be modified by leaving group conjugates of R^(C) (i.e. LG-R^(C),wherein LG is a leaving group as defined herein) as an alternative tointroduction of R^(C) through intermediate S-7. Alternative orders ofassembly for the various synthetic intermediates into compounds ofFormula (I) are contemplated.

When linker of X¹ are alkyl, alternate methods of constructing thelinkage to compounds S-6 are utilized (see Scheme 2). An organometalspecies S-8 wherein Mx is a metal or metalloid (e.g. magnesium, lithium,zinc, boron, tin, or silicon) can be utilized to displace the halide X³of compounds S-6 to generate compounds of Formula (I). In certainembodiments, the reaction conditions may comprise a transition metalcatalyst; e.g. palladium, nickel. In certain embodiments, the reactionconditions may comprise a ligand; e.g. a phosphine ligand such asX-phos. Alternatively, the metal species S-9 can be used to couple to ordisplace halides of S-10 (see Scheme 3). Alternative orders of assemblyfor the various synthetic intermediates into compounds of Formula (I)are contemplated.

Compounds of Formula (II) can be prepared using methods analogous to themethods described in Schemes 1 to 3, except that compound S-7, S-8, andS-10 are replaced with compounds S-11, S-12, and S-13, respectively:

Non-limiting examples of the preparation of exemplary compoundsdescribed herein are illustrated in Examples 1 to 3.

Example 1 Preparation of2-((2-methoxy-4-(4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl)phenyl)(methyl)amino)-5,11-dimethyl-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-6(11H)-one

4-((5,11-Dimethyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)(methyl)amino)-3-methoxybenzoicacid (27.8 mg, 0.0663 mmol, 1 eq) was dissolved in DMF (1.4 mL). HATU(28.7 mg, 0.0754 mmol, 1.1 eq) and DIPEA (23.9 microliters, 0.137 mmol,2 eq) were added, followed by 1-methyl-4-(piperidin-4-yl)piperazine(15.1 mg, 0.0823 mmol, 1.2 eq). After 15 hours, the mixture was dilutedwith aqueous sodium bicarbonate and extracted with DCM and EtOAc. Thecombined organic layer was dried over sodium sulfate, filtered andcondensed. Purification by column chromatography (ISCO, 4 g silicacolumn, 0-15% MeOH/DCM, 15 minute gradient) gave the product as a whitesolid (30.06 mg, 0.0514 mmol, 78%). ¹H NMR (400 MHz, Methanol-d₄) δ 8.07(s, 1H), 7.71 (dd, J=7.9, 1.7 Hz, 1H), 7.51-7.43 (m, 1H), 7.30 (d, J=7.9Hz, 1H), 7.17-7.10 (m, 3H), 7.03 (dd, J=7.9, 1.7 Hz, 1H), 4.65 (s, 1H),3.92 (s, 1H), 3.78 (s, 3H), 3.43 (s, 3H), 3.40 (s, 3H), 3.22 (d, J=19.9Hz, 4H), 2.90 (s, 2H), 2.79-2.56 (m, 8H), 2.42 (s, 3H), 2.01 (s, 1H),1.90 (s, 1H), 1.52 (s, 2H). ¹³C NMR (100 MHz, cd₃od) δ 170.36, 169.05,163.86, 158.32, 155.62, 151.12, 149.75, 135.46, 134.96, 132.45, 131.33,129.03, 126.10, 123.27, 119.61, 118.94, 117.26, 110.65, 72.42, 63.00,61.16, 54.93, 54.90, 54.30, 43.95, 37.12, 37.09, 36.93, 36.91, 34.36,28.49, 27.63. LCMS 585.60 (M+H).

Example 2 Preparation of2-(ethyl(2-methoxy-4-(4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl)phenyl)amino)-5,11-dimethyl-5H-benzo[e]pyrimido[5,4-b][1, 4]diazepin-6(11H)-one

4-((5,11-Dimethyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)(ethyl)amino)-3-methoxybenzoicacid (12.4 mg, 0.0286 mmol, 1 equivalent) was dissolved in DMF (0.57mL). HATU (11.9 mg, 0.0314 mmol, 1.1 eq) and DIPEA (10 microliters,0.0571 mmol, 2 eq) were added, followed by1-methyl-4-(piperidin-4-yl)piperazine (6.3 mg, 0.0343 mmol, 1.2 eq).After 18 hours, the mixture was diluted with aqueous sodium bicarbonateand extracted with DCM and EtOAc. The combined organic layer was driedover sodium sulfate, filtered and condensed. Purification by preparativeHPLC, followed by free basing gave the product as a white solid (9.77mg, 0.0163 mmol, 57%). ¹H NMR (400 MHz, Methanol-d₄) δ 8.06 (s, 1H),7.72 (dd, J=8.0, 1.7 Hz, 1H), 7.54-7.45 (m, 1H), 7.28 (d, J=7.9 Hz, 1H),7.15 (t, J=7.2 Hz, 2H), 7.12 (d, J=1.7 Hz, 1H), 7.04 (dd, J=7.9, 1.7 Hz,1H), 4.66 (s, 1H), 3.94 (s, 3H), 3.77 (s, 3H), 3.44 (s, 3H), 3.28-3.10(m, 4H), 2.92 (d, J=25.6 Hz, 2H), 2.77-2.46 (m, 8H), 2.31 (s, 3H), 1.91(s, 1H), 1.51 (s, 2H), 1.23-1.18 (m, 3H). ¹³C NMR (100 MHz, cd₃od) δ171.81, 170.52, 165.37, 159.32, 157.47, 152.61, 151.24, 137.02, 134.86,133.84, 132.75, 131.29, 127.57, 124.70, 120.92, 120.29, 118.61, 112.03,64.44, 62.74, 56.29, 55.93, 46.26, 45.87, 38.47, 35.76, 14.46, 13.42.LCMS 599.56 (M+H).

Example 3 Preparation of3-(cyclopentyloxy)-4-((5,11-dimethyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)benzoicacid

Methyl3-(cyclopentyloxy)-4-((5,11-dimethyl-6-oxo-6,11-dihydro-5H-benzo[e]pyrimido[5,4-b][1,4]diazepin-2-yl)amino)benzoate(9.35 mg, 0.0197 mmol, 1 eq) and LiOH (1.4 mg) was dissolved in THF (0.2mL) and water (0.1 mL). After 16 hours, the mixture was diluted withMeOH and purified by preparative HPLC to give an off-white solid (3.35mg). ¹H NMR (400 MHz, Methanol-d₄) δ 8.51 (d, J=8.5 Hz, 1H), 8.19 (s,1H), 7.75 (dd, J=7.9, 1.7 Hz, 1H), 7.70 (dd, J=8.5, 1.8 Hz, 1H), 7.55(d, J=1.8 Hz, 1H), 7.48-7.42 (m, 1H), 7.14 (dd, J=7.7, 5.6 Hz, 2H), 4.94(tt, J=5.1, 2.3 Hz, 1H), 3.48 (s, 3H), 3.46 (s, 3H), 2.05-1.89 (m, 4H),1.88-1.78 (m, 2H), 1.72-1.62 (m, 2H). LCMS 460.36 (M+H).

Example 4 Biochemical and Cellular Assays of the CompoundsAcetyl-Histone Binding Assay

Assays were performed with minor modifications from the manufacturer'sprotocol (PerkinElmer, USA). All reagents were diluted in 50 mM HEPES,150 mM NaCl, 0.1% w/v BSA, and 0.01% w/v Tween 20 at pH 7.5 and allowedto equilibrate to room temperature prior to addition to plates. Afteraddition of Alpha beads to master solutions, all subsequent steps wereperformed in low light conditions. A 2× solution of components withfinal concentrations of BRD4.1 at 80 nM, Ni-coated Acceptor Bead at 25μg/ml, and 80 nM biotinylated H4-tetra acetyl was added in 10 μL to384-well plates (AlphaPlate—384, PerkinElmer, USA). Biotinylated peptidefor BRD4.1 was synthesized in-house on a CEM Liberty 9008005 microwavepeptide synthesizer: H4-tetra acetyl,biotin-PEG2-SGRGKacGGKacGLGKacGGAKacRHRK-COOH. Addition to wells wasperformed with either a multichannel pipet (for optimizationexperiments) or a Biotek EL406 liquid handler. After a 1000-rpmspin-down for 1 minute, 100 nL of the solutions of the compounds of theinvention from stock plates were added by pin transfer using a JanusWorkstation (PerkinElmer, USA). The streptavidin-coated donor beads (25μg/ml final) were added as with previous solution in a 2×, 10 μL volume.Following this addition, the plates were sealed with foil to block lightexposure and to prevent evaporation. The plates were spun down again at1000 rpm for 1 minute. Next, the plates were incubated in the room withthe plate reader (for temperature equilibration) for 1.5 hour prior toreading the assay. AlphaScreen measurements were performed on anEnvision 2104 (PerkinElmer, USA) utilizing the manufacturer's protocol.

Cellular Assay

The compounds of the invention are also evaluated in the BRD4 dependantcell line for the cellular activity to generate cellular IC₅₀ values.

Cells (e.g., BRD4 dependant cells) were counted and adjusted to 60,000cells/mL. Using a Biotek EL406, 50 μL of the cells in media weredistributed into 384 well white plates from Thermo. Immediately afterplating, compounds of the invention in DMSO were distributed to plates.For large plate sets, cells were returned to a 37° C. incubator whilenot in use. The compounds were added to plates using a 100 nL 384 wellpin transfer manifold on a Janus workstation. Stocks were arrayed in 10point quadruplicate dose response in DMSO stock in 384-well Greinercompound plates. After addition of the compounds, plates were incubatedfor three days in a 37° C. incubator. Cell viability was read out usingATPlite from Perkin Elmer. Plates were removed from the incubator andbrought to room temperature prior to use. Lyophilized powder wasresuspended in lysis buffer and diluted 1:2 with DI water. 25 μL of thissolution was added to each well using the Biotek liquid handler. Plateswere sealed with adherent aluminum seals prior to vortexing and spinningdown at 1000 g for 1 minute. Plates were incubated for 15 minutes atroom temperature before signal was read on an Envision Plate Reader.

Isothermal Titration Calorimetery

ITC was performed using a ITC200 microcalorimeter from GE™ (Northampton,Mass.). All experiments were carried out at 25° C. while stirring at1000 rpm, in ITC buffer (50 mM HEPES pH 7.4 at 25° C., 150 mM NaCl). Themicrosyringe was loaded with a solution of the protein sample (225 μM,in ITC buffer). The compound solution (22.5 μM, in ITC buffer) wastitrated into the protein solution via syringe. All titrations wereconducted using an initial injection of 0.2 μl, followed by 19 identicalinjections of 2 μl with a duration of 5 sec (per injection) and aspacing of 90 sec between injections. The heat of dilution wasdetermined by independent titrations (protein into buffer) and wassubtracted from the experimental data. The collected data wereimplicated in the MicroCal™ Origin software supplied with the instrumentto yield enthalpies of binding (ΔH) and binding constants (K_(a)). Thecollected data were implicated in the MicroCal™ Origin software suppliedwith the instrument to yield enthalpies of binding (ΔH) and bindingconstants (K_(B)) as previously described by Wiseman and coworkers.Thermodynamic parameters were calculated (ΔG=ΔH−TΔS=−RT ln K_(B), whereΔG, ΔH and ΔS are the changes in free energy, enthalpy and entropy ofbinding respectively). A single binding site model was employed.

Cell Cycle Analysis by Flow Cytometry

797, MOLM-13, and HL60 cells were plated in T-75 flasks and grown inDMEM (797) or RPMI (MOLM-13 and HL60) containing 10% fetal bovine serumand 1% penicillin/streptomycin. Cells were treated with compound at 1 uM(797) or 500 nM (MOLM-13 and HL60), or the equivalent volume of DMSO for24 hours. 2×106 cells were spun at 500×g for minutes at 4° C. and washedwith PBS. Pellets were resuspended in 1 mL of cold PBS and addeddropwise while gently vortexing to 9 mL 70% ethanol in a 15 mLpolypropylene centrifuge tube. Fixed cells were then frozen at −20° C.overnight. The next day, cells were centrifuged at 500×g for 10 minutesat 4° C. and washed with 3 mL of cold PBS. Cells were resuspended in 500μL of propidium iodide staining solution (0.2 mg/mL RNAse A, 0.2 mg/mLpropidium iodide, 01.% Triton-X in PBS) and incubated for 20 min at 37°C. Samples were then transferred to ice and analyzed on a BD FACS CantoII. Histograms were generated and cell cycle analysis was performedusing ModFit flow cytometry analysis software.

Results

Shown in Table 1 are exemplary in vitro percent inhibition values ofBRD4.1 at 2.5 μM compound concentration for exemplary compounds, where“uM” refers to micromolar, and “% INHIB” refers to % inhibition.

TABLE 1 % INHIB Structure (at 2.5 uM)

20.5

45.8

36.1

29.5

50.8

Shown in Table 2 are exemplary IC₅₀ values of select compounds describedherein and compounds JQ1 and GSK461364 against selectbromodomain-containing proteins, kinases, and cell lines. “uM”: μM.

TABLE 2 Compound IC₅₀ 1-226 BRD4 IC₅₀ = 303 nM BRDT IC₅₀ = 2,110 nM BRD4IC₅₀ = 488 nM LRRK2 IC₅₀ = 7 nM MV411 IC₅₀ = 549 nM NOMO1 IC₅₀ = 2 uMKasumi-1 IC₅₀ = 393 uM TF-1 IC₅₀ = 3.36 uM MOLM-13 IC₅₀ = 1.27 uM 797IC₅₀ = 1,304 nM 1-284 BRD4 IC₅₀ = 1,987 nM BRDT IC₅₀ = 5,546 nM BRD4IC₅₀ = 2.6 uM LRRK2 IC₅₀ = 4.0 uM MV411 IC₅₀ = 2,437 nM NOMO1 IC₅₀ = 8.6uM Kasumi-1 IC₅₀ = 1.86 uM TF-1 IC₅₀ = 6.16 uM MOLM-13 IC₅₀ = 4.63 uM797 IC₅₀ = 7,417 nM 2-041 BRD4 IC₅₀ = 2.060 nM BRDT IC₅₀ = 9,608 nM BRD4IC₅₀ = 5.7 uM LRRK2 IC₅₀ = 3.0 uM MV411 IC₅₀ = 3,476 nM NOMO1 IC₅₀ = 8.3uM Kasumi-1 IC₅₀ = 2.36 uM TF-1 IC₅₀ = 7.21 uM MOLM-13 IC₅₀ = 5.74 uM797 IC₅₀ = 7,100 nM 2-043 BRD4 IC₅₀ = 732 nM BRDT IC₅₀ = 2,728 nM BRD4IC₅₀ = 1.51 uM MV411 IC₅₀ >10 uM NOMOI IC₅₀ = 6.8 uM Kasumi-1 IC₅₀ =4.78 uM TF-1 IC₅₀ = 7.1 uM MOLM-13 IC₅₀ = 6,61 uM 797 IC₅₀ = 1,788 nM2-075 BRD4 IC₅₀ = 970 nm BRDT IC₅₀ = 2,879 nM BRD4 IC₅₀ = 1.80 uM CREBBPIC₅₀ = 431 nM BRD4 K_(D) = 180 nM (DiscoveRx) CREBBP K_(D) = 23 nM(DiscoveRx) MV411 IC₅₀ = 252 nM NOMO1 IC₅₀ = 2.5 uM Kasumi-1 IC₅₀ = 96nM TF-1 IC₅₀ = 2.14 uM MOLM-13 IC₅₀ = 433 nM 797 IC₅₀ = 34 nM

BRD4 IC₅₀ = 44 nM BRDT IC₅₀ = 147 nM MV411 IC₅₀ = 65.6 nM NOMO1 IC₅₀ =172 nM Kasumi-1 IC₅₀ = 48.8 nM TF-1 IC₅₀ = 109 uM MOLM-13 IC₅₀ = 89.2 nM797 IC₅₀ = 92 nM JQ1

BRD4 IC₅₀ >50 uM BRDT IC₅₀ >50 uM MV411 IC₅₀ = 7.1 nM NOMO1 IC₅₀ = 5.91nM Kasumi-1 IC₅₀ = 7.8 nM TF-1 IC₅₀ = poor convergence MOLM-13 IC₅₀ =6.93 nM 797 IC₅₀ = 8 nM GSK461364

1. A method of treating a disease associated with a bromodomain orbromodomain-containing protein in a subject in need thereof, the methodcomprising administering to the subject a therapeutically effectiveamount of a compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring. 2-3.(canceled)
 4. A method of treating a disease associated with aberrantactivity of a bromodomain or bromodomain-containing protein in a subjectin need thereof, the method comprising administering to the subject atherapeutically effective amount of a compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring. 5-10.(canceled)
 11. A method for male contraception, the method comprisingadministering to a subject in need thereof an effective amount of acompound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring.
 12. A methodof inhibiting the activity of a bromodomain or bromodomain-containingprotein in a subject or cell, the method comprising administering to thesubject or contacting the cell with an effective amount of a compound ofFormula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(═O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring.
 13. Themethod of claim 12, wherein the activity of the bromodomain-containingprotein is selectively inhibited by the method, compared to the activityof a kinase. 14-15. (canceled)
 16. A method of inhibiting the binding ofa bromodomain of a bromodomain-containing protein to an acetyl-lysineresidue of a second protein in a subject or cell, the method comprisingadministering to the subject or contacting the cell with an effectiveamount of a compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein: the secondprotein is a protein that comprises at least one acetyl-lysine residueand is different from the bromodomain-containing protein;

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring.
 17. Themethod of claim 16, wherein the second protein is a histone.
 18. Amethod of modulating the expression of a gene that is regulated by abromodomain-containing protein in a subject or cell, the methodcomprising administering to the subject or contacting the cell with aneffective amount of a compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(═O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring.
 19. Themethod of claim 18, wherein the transcription of the gene is modulatedby the method.
 20. A method of inhibiting the expression of a gene thatis regulated by a bromodomain-containing protein in a subject or cell,the method comprising administering to the subject or contacting thecell with an effective amount of a compound of Formula (II):

or a pharmaceutically acceptable salt thereof, wherein:

is a single or double bond; W is —C(═O)OR^(Z1), —C(═O)N(R^(Z1))₂,—S(═O)OR^(Z1), —S(═O)N(R^(Z1))₂, —S(═O)₂OR^(Z1), —S(═O)₂N(R^(Z1))₂, or

Z is —O—, —N(R^(Z))— or —C(R^(Z))₂—, wherein each instance of R^(Z) isindependently hydrogen, halogen, substituted or unsubstituted acyl,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(Z1), —SR^(Z1), —N(R^(Z1))₂, or a nitrogen protectinggroup when attached to a nitrogen atom, or two instances of R^(Z) arejoined to form a substituted or unsubstituted carbocyclic or substitutedor unsubstituted heterocyclic ring; each instance of R^(Z1) isindependently hydrogen, substituted or unsubstituted acyl, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, an oxygenprotecting group when attached to an oxygen atom, a sulfur protectinggroup when attached to a sulfur atom, or a nitrogen protecting groupwhen attached to a nitrogen atom, or two instances of R^(Z1) are joinedto form a substituted or unsubstituted heterocyclic or substituted orunsubstituted heteroaryl ring; each instance of R^(A) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(A1), —N(R^(A1))₂, —SR^(A1), —CN, —SCN,—C(═NR^(A1))R^(A1), —C(═NR^(A1))OR^(A1), —C(═NR^(A1))N(R^(A1))₂,—C(═O)R^(A1), —C(═O)OR^(A1), —C(═O)N(R^(A1))₂, —NO₂,—NR^(A1)C(═O)R^(A1), —NR^(A1)C(═O)OR^(A1), —NR^(A1)C(═O)N(R^(A1))₂,—OC(═O)R^(A1), —OC(═O)OR^(A1), or —OC(═O)N(R^(A1))₂, wherein eachinstance of R^(A1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(A1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; n is 0, 1, 2, 3, 4, 5, 6,7, or 8; X is absent, —C(═O)—, or —C(R^(X))₂—, wherein each instance ofR^(X) is independently hydrogen, halogen, or substituted orunsubstituted C₁₋₆ alkyl; each instance of R^(B) is independentlyhydrogen, halogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, —OR^(B1), —N(R^(B1))₂, —SR^(B1), —CN, —SCN,—C(═NR^(B1))R^(B1), —C(═NR^(B1))OR^(B1), —C(═NR^(B1))N(R^(B1))₂,—C(═O)R^(B1), —C(═O)OR^(B1), —C(═O)N(R^(B1))₂, —NO₂,—NR^(B1)C(═O)R^(B1), —NR^(B1)C(═O)OR^(B1), —NR^(B1)C(═O)N(R^(B1))₂,—OC(═O)R^(B1), —OC(═O)OR^(B1), or —OC(═O)N(R^(B1))₂, wherein eachinstance of R^(B1) is independently hydrogen, substituted orunsubstituted acyl, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, a nitrogen protecting group when attached to a nitrogenatom, an oxygen protecting group when attached to an oxygen atom, or asulfur protecting group when attached to a sulfur atom, or two R^(B1)groups are joined to form a substituted or unsubstituted heterocyclic orsubstituted or unsubstituted heteroaryl ring; m is 0, 1, 2, 3, or 4;R^(C) is hydrogen or substituted or unsubstituted C₁₋₆ alkyl; R^(D) ishydrogen or substituted or unsubstituted alkyl; R^(E) is hydrogen orsubstituted or unsubstituted alkyl; R^(F) is hydrogen, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted carbocyclyl, substituted or unsubstituted heterocyclyl,substituted or unsubstituted aryl, or substituted or unsubstitutedheteroaryl; R^(G) is hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedcarbocyclyl, substituted or unsubstituted heterocyclyl, substituted orunsubstituted aryl, or substituted or unsubstituted heteroaryl; andR^(H) is hydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted carbocyclyl,substituted or unsubstituted heterocyclyl, substituted or unsubstitutedaryl, or substituted or unsubstituted heteroaryl; or R^(G) and R^(H) arejoined to form a substituted or unsubstituted phenyl ring.
 21. Themethod of claim 20, wherein the transcription of the gene is inhibitedby the method.
 22. The method of claim 1, wherein thebromodomain-containing protein is a bromo and extra terminal (BET)protein.
 23. The method of claim 1, wherein the bromodomain-containingprotein is bromodomain-containing protein 2 (BRD2),bromodomain-containing protein 3 (BRD3), or bromodomain-containingprotein 4 (BRD4).
 24. The method of claim 1, wherein thebromodomain-containing protein is a TBP (TATA box bindingprotein)-associated factor protein (TAF).
 25. (canceled)
 26. The methodof claim 1, wherein the bromodomain-containing protein is CREB-bindingprotein (CBP) or E1A binding protein p300 (EP300).
 27. (canceled) 28.The method of claim 1, wherein the disease is a proliferative disease.29-32. (canceled)
 33. The method of claim 1, wherein the disease is aninflammatory disease, a cardiovascular disease, an autoimmune disease, aviral infection, a fibrotic disease, a metabolic disease, or anendocrine disease. 34-102. (canceled)
 103. A compound of the formula:

or a pharmaceutically acceptable salt thereof.
 104. (canceled)
 105. Apharmaceutical composition comprising a compound of claim 103, or apharmaceutically acceptable salt thereof, and optionally apharmaceutically acceptable excipient.
 106. A kit comprising: a compoundof claim 103, or a pharmaceutically acceptable salt thereof, andinstructions for using the kit.